J.P. Morgan Healthcare Conference January 2015

J.P. Morgan Healthcare Conference January 2015 1

Safe Harbor Provisions SAFE HARBOR PROVISIONS FOR FORWARD-LOOKING STATEMENTS: This news release may contain forward-looking statements within the meaning of the federal securities laws. Statements regarding future events, developments, the Company's future performance, as well as management's expectations, beliefs, intentions, plans, estimates or projections relating to the future (including, without limitation, statements concerning revenue and net income), are forward-looking statements within the meaning of these laws and involve a number of risks and uncertainties. Management believes that these forward looking statements are reasonable and are based on reasonable assumptions and forecasts, however, undue reliance should not be placed on such statements that speak only as of the date hereof. Moreover, these forward-looking statements are subject to a number of risks and uncertainties, some of which are outlined below. As a result, actual results may vary materially from those anticipated by the forward-looking statements. Among the important factors that could cause actual results to differ materially from those indicated by such forward-looking statements are: the volume and timing of systems sales and installations; length of sales cycles and the installation process; the possibility that products will not achieve or sustain market acceptance; seasonal patterns of sales and customer buying behavior; impact of incentive payments under The American Recovery and Reinvestment Act on sales and the ability of the Company to meet continued certification requirements; the development by competitors of new or superior technologies; the timing, cost and success or failure of new product and service introductions, development and product upgrade releases; undetected errors or bugs in software; product liability; changing economic, political or regulatory influences in the health-care industry; changes in product-pricing policies; availability of third-party products and components; competitive pressures including product offerings, pricing and promotional activities; the Company's ability or inability to attract and retain qualified personnel; possible regulation of the Company's software by the U.S. Food and Drug Administration; uncertainties concerning threatened, pending and new litigation against the Company including related professional services fees; uncertainties concerning the amount and timing of professional fees incurred by the Company generally; changes of accounting estimates and assumptions used to prepare the prior periods' financial statements; general economic conditions; and the risk factors detailed from time to time in the Company s periodic reports and registration statements filed with the Securities and Exchange Commission. 2

Company Overview Quality Systems, Inc. and its NextGen Healthcare subsidiary develop and market computer-based practice management, electronic health records (EHR) and revenue cycle management applications, as well as connectivity products and services, for medical and dental group practices and small hospitals. Revenue primarily derived from physician group businesses that utilize the Company s high functionality practice management suites Focus is on growing organically with a strong emphasis on reinvestment in new product and service development initiatives Acquisitions of complementary business lines are also key drivers of growth 3

Organizational Timeline A willingness to reinvest and reinvent to better compete 4

Quality Systems Today September 30 th, 2014 TTM Revenue: $462.5mm Non-GAAP EPS: $0.49 TTM Revenue: $359.3mm (78% of total) TTM Revenue: $18.9mm (4% of total) TTM Revenue: $70.3mm (15% of total) TTM Revenue: $13.8mm (3% of total) 80,000 + Physicians 10,000 + Dentists 6,500 + Physicians 300 + Hospitals Markets Served: Physicians Practice Management Electronic Health Records EDI Markets Served: Dentists Practice Management Electronic Dental Record EDI Markets Served: Physicians Revenue Cycle Management Other Services Markets Served: Small Hospitals Financials Clinical Surgery Scheduling 5

Market Drivers American Recovery and Re-investment Act (ARRA) 2/09 Over $60 billion in incentive and grant money to stimulate healthcare information technology (HIT) adoption. Stringent rules for providers to qualify for funds known as Meaningful Use First time that state-based Medicaid programs and Departments of Health become major purchasers of HIT Regional Extension Center initiative promoting large scale HIT adoption Pay-for-performance (P4P) programs, patient-centered medical home, and other quality initiatives Consumerism and Personal Health Records (PHR) Interoperability and community-based data exchange Market mindset has moved to when not if 6

Medicare Complete EHR EP Attestations Top Ten Vendors Epic Systems Corporation 98,201 Allscripts 49,683 eclinicalworks LLC 39,701 NextGen Healthcare 37,514 GE Healthcare 29,026 Greenway Medical Technologies, Inc. 22,296 Cerner Corporation 18,438 Practice Fusion 14,798 athenahealth, Inc 11,532 McKesson 11,491-20,000 40,000 60,000 80,000 100,000 120,000 Based on CMS September 2014 attestation data 7

Medicare Complete EHR EP Attestations: Top Vendors by % Total All Other 27% EPIC 22% McKesson 3% Allscripts 11% athenahealth, Inc 3% Practice Fusion 3% Cerner Corporation 4% Greenway Medical Technologies 5% GE Healthcare 6% NextGen 8% eclinicalworks LLC 9% The top five vendors continue to dominate more than half (56%) of all attestations, where All Other represents a collection of almost 500 additional vendors Based on CMS September 2014 attestation data 8

Hospital Attestations: Top Vendors by % Total MEDITECH 21% EPIC 16% NextGen 2% Midas+ / ACS 2% Iatric 2% T-Systems 2% Community Health Systems 2% ProMed 2% AllOther 18% HCA 3% Based on CMS September 2014 attestation data Allscripts 4% Healthland 5% Siemens 5% MEDHOST 8% Cerner Corporation 15% CPSI 10% McKesson 10% 9

EHR Incentive Program Total Program to Date Stage 1 Payments Active Registrations Providers Paid Dollars Paid Medicare Eligible Professionals 323,050 264,921 $6.42 Billion Medicaid Eligible Professionals 160,075 128,049 $3.21 Billion Eligible Hospitals 4,741 4,071 $12.83 Billion Total 487,866 397,041 $22.46 Billion Stage 2 Payments Providers Paid Dollars Paid Medicare Eligible Professionals 795 $5.13 Million Eligible Hospitals 4 $552,382 Total 799 $5.68 Million Total Dollars Paid $22.47 Billion Based on ONC July 2014 data 10

Re-Ranking the Top 10 by Year 3 Success Rate Payment Year 1, 2011 Payment Year 2, 2012 Payment year 3, 2013 Top Ten Vendors In Descending Order of Year 3 Attestations Epic Systems Corporation 12,587 Allscripts 4,923 eclinicalworks LLC 3,669 NextGen Healthcare 2,888 Greenway Health, Inc. 2,794 GE Healthcare 2,631 athenahealth, Inc. 1,663 Community Computer Services 1,196 Practice Fusion 1,191 Top Ten Vendors In Descending Order of Success Rate Epic Systems Corporation 92.78% athenahealth, Inc. 91.22% NextGen Healthcare 88.48% GE Healthcare 84.63% Allscripts 81.86% Greenway Health, Inc. 81.01% Community Computer Services 80.32% eclinicalworks LLC 79.43% e-mds, Inc. 75.21% e-mds, Inc. 1,007 Practice Fusion 74.91% NextGen Healthcare maintains the #3 ranking based on Year 3 success rates Average Year3 success rate of all included vendors (178 total): 69% Average Year3 Success rate of Top Ten Vendors: 83% Based on ONC July 2014 data 11

Market Opportunity & Positioning Growth High Growth Low Growth Dental Software <$ 1 Billion <100 Bed Hospital Software $1-2 Billion 60-70% Penetrated Ambulatory Software $6 Billion 60-70% Penetrated Revenue Cycle Management Services $50 Billion 20-25% Penetrated 80% Penetrated Low Opportunity (High Penetration) Penetration Opportunity High Opportunity (Low Penetration) 12

Representative Customers 13

Accountable Care Organizations 14

Revenue & Earnings Growth Opportunities Continued growth of our core businesses Cross selling of complementary products Significantly expand on RCM services capabilities Leverage Mirth acquisition to enhance our HIE, Population Health, and ACO strategy Grow Dental with our new cloud-based product with strategic partnerships Continue to make strategic acquisitions Leverage and expand our offshore R&D capabilities 15

Strategic Dial Movers Continued Growth of Our Core Businesses This is the third year of government incentive payments to physicians and hospitals with half of the market to go Stage 1-2-3 Resale Market ICD 9-10-11 Resale Market Healthcare Reform Five Years of Incentives Five Years of Penalties 10 Year Adoption Period 16

Strategic Dial Movers Focusing on Opportunities to Sell Complementary Products There is significant opportunity in cross-selling new solutions to the existing customer base and bundling multiple solutions for new customers (RCM, Mirth, Population Health, etc.) Large Installed Base 90,000 Physicians 10,000 Dentists 325 Hospitals Four Divisions 20 Product Offerings 17

Product Penetration in Current Client Base Creating demand for ancillary products Focused on client education, product bundling, and marketing Client base demand for products is significant 100% EPM EHR Patient Portal Dashboard NextPen EHR Connect RCM HIE Population Health 94% 89% 39% 0% Product Penetration 13% 12% Green Field Opportunities 5% 5% 1% < 1% 18

Strategic Dial Movers Expand Revenue Cycle Management Capabilities NextGen RCM has been set-up to grow the company s RCM business and is already seeing strong results. With plans to expand into dental and hospital markets. Reform Provides the Fuel Core vs. Non-Core Competency Reimbursement Pressure Revenue Down Regulatory Pressure Costs Up 19

20 Quick Fact

Majority of Practices See Results (with RCM) Source: MGMA. Medical Billing Services Information Exchange: #4840. Based on MGMA Survey: Medical Billing Companies Produce Strong Results, 2009. (http://www.mgma.com/store/book s/medical-billing-services/) 21

Revenue Cycle Management is a $50 Billion Market in the United States Revenue cycle management (RCM) is currently a $50 billion market in the US 7.5 Times Larger than the EHR Market Source: Frost & Sullivan 2013 22

Momentum/Opportunities in RCM Services $69.5 (1) million in revenue (TTM through Q2 FY 2015), representing 15% of total QSI revenue and 16.6% growth rate YoY #1 ranking in KLAS 2014 Ambulatory RCM services survey Only 5% penetration into existing NextGen Ambulatory client base Industry trends driving RCM outsourcing Regulatory & Compliance (ICD-10, 11) Provider reimbursement continues to decline Large shift to patient payment responsibility making collections more difficult (1) excludes HMA revenues for corresponding periods 23

Recent RCM Services Wins Capital Women s Care 10 year RCM renewal Tenet Health System University Orthopedic Center Jordan Valley Health Center 24

The Mirth Plan Headquartered in Costa Mesa, CA 70 employees Acquired September 2013 Experts in Healthcare Data Integration and Health Information Exchange Global leader in commercial and open source software for Health IT Focused exclusively on healthcare software for 14 years Revolutionizing how organizations adapt to evolving HIT requirements and push towards interconnected healthcare Family of Mirth products connect seamlessly and naturally within the HIT ecosystem Solution to satisfy demands from HIEs and the emergence of ACOs 1993 1999 2006 Software Development Healthcare Focus Mirth Products 25

Mirth Drivers Health Information Exchange (HIE) and interoperability in heavy demand. Public and private HIEs continue their build-out. Population Health Management requires robust HIE and central data repository as backbone infrastructure. Value-driven healthcare organizations deploying HIE and central data repository capabilities to aggregate clinical, financial and administrative data to drive analytics and care coordination. DIRECT messaging solutions seeing robust uptake. 26

The Mirth Solution Mirth Results Central Data Repository Document Factory (C-CDA) Provider Portal IHE: PIX/PDQ, XDS.b, etc Consent & Confidential Info Mirth Mail Secure Direct Messaging, Chat, & Provider Directory Mirth Care Chronic Disease Management & Care Management Mirth Match EMPI & Record Locator Service Mirth Connect Data Integration Engine Mirth Analytics Business Intelligence, Reporting, & Analytics Direct Messaging, Secure Chat, HPD+ Provider Directory HL7, DiCOM, X12, CCD, C-CDA, EHR Integration 27

Mirth Momentum Ahead of internal projections Strong interest in Mirth Care Enterprise, our population health solution for chronic disease management Recently announced agreement with Health Information Network of Arizona (HINAz), Arizona s statewide HIE, to elevate interoperability services and care coordination across health care systems and among health care providers throughout the state This is the first statewide HIE 28

Momentum in Dental & EDI Significant growth with QSIDental Web, QSI Dental s SAAS cloud offering released in mid 2012. Pacific Dental Services has selected QSIDental Web to roll out across its enterprise of 400 supported dental practices Strategic partnership with Patterson Dental as part of a special markets referral agreement Significant opportunity in moving existing legacy software install base to QSIDental Web New EDI products for sale to existing install base 29

Strategic Dial Movers Continued Growth through Acquisitions QSI is focused on bolt-on acquisitions to fill a strategic gap or kick-start entry into newer business lines Nine Acquisitions in Last Four Years RCM Analytics Patient Management Regulatory and Clinical Reporting Tools 30

Strategic Dial Movers Expand Offshore Capabilities to Capture Cost Efficiencies Opened in Bangalore, India in July 2011 Currently employing over 325 FTE s in R&D and QA Using labor arbitrage to reduce costs 31

Better Alignment of Sales & Marketing Stabilized the sales team Strong industry experience; 5 years on average for Sales Executives Increasing headcount in FY14 to support RCM; Inside Sales and Small Practice Integrated sales and marketing across all divisions Reorganized the sales team to: Take advantage of industry trends Align the team s strengths with industry trends RCM Services Professional Consulting Services Ambulatory fringe markets Cross selling within the current client base Multi-product net new sales Opened up the pricing playbook to support growth models 32

Financial Highlights TTM Sept 2014 FYE (1) 2014 FYE 2013 FYE 2012 FYE 2011 FYE 2010 Revenue $462,470 $444,667 $460,229 $429,835 $353,363 $ 291,811 Net income* $19,869 $33,022 $59,124 $75,657 $61,606 48,379 Diluted earnings per share * $0.33 $0.55 $0.99 $1.28 $1.06 $0.84 Cash dividends declared per share $0.70 $0.70 $0.70 $0.70 $0.63 $0.60 Total Shareholders Equity $285,381 $295,090 $307,050 $295,177 $224,670 $ 188,289 (in thousands, except per share amounts) (1) FYE March 31 st *TTM and 2014 Net Income and Diluted Earnings per Share exclude $26 million impairment charge and estimated tax impact in Q3 2014, 2013 Net Income and Diluted Earnings per Share exclude $17.4 million impairment charge and estimated tax impact of such charge A proven record of delivering value back to Shareholders 33

Why Quality Systems? Proven Growth and Profitability Robust Sales Pipeline Proven track record of organic growth Five-year revenue CAGR of 11% Self-funded, highly profitable growth strategy Recurring revenue represented 81% of total revenue in FY 2014 Cash and marketable securities of $123.5 million and no debt $0.70 dividend per share (Yield of 4.5% based on 1/6/15 share price of $15.64) (1) $162 million NextGen Healthcare sales pipeline @ 9/30/14 Lead Generation up year over year Substantial Customer Base Over 4,400 group practices representing 90,000 physicians and dentists 325 hospital relationships Leading Suite of HCIT Products Certified technology platform in hospital, physician and dental markets Positive HCIT Industry Trends Experienced Management Team Increasing focus on technology benefits in healthcare Healthcare Reform Economic Stimulus Package/Obama Plan from U.S. Government Extensive years of experience and working collaboratively as a management team (1) Dividends are declared quarterly at the discretion of the board of directors 34

18111 Von Karman Avenue Suite 700 Irvine, California 92612 (949) 255-2600 Phone www.qsii.com www.nextgen.com Daniel J. Morefield Chief Operating Officer dmorefield@qsii.com Mark Davis Executive Vice President, Corporate Development & Strategy mdavis@qsii.com Steven T. Plochocki Chief Executive Officer splochocki@qsii.com Paul A. Holt Executive Vice President & Chief Financial Officer pholt@qsii.com Susan Lewis Investor Relations slewis@qsii.com 35