The implementation of the Chronic Disease Management Program or PROLANIS has been adopted in Indonesia by National Social Security Implementation on Health Agency (BPJS-K) since 2015. The program focuses on hypertension (HT) and diabetes mellitus (DM). However, since the first time the program was implemented, there was no comprehensive evaluation of it. The aim of this study was to analyze health service quality among HT and DM patients based on five dimensions of quality in 25 community health services (CHSs) in the Sleman district, Yogyakarta, Indonesia. This is a cross-sectional study with a simple random sampling technique that included 230 respondents from 25 CHSs. The instrument was SERVQUAL that consisted of 35 items of a questionnaire. The data were analyzed by a gap analysis, Customer Satisfaction Index (CSI) and Importance Performance Analysis (IPA); meanwhile, a Man–Whitney test was proposed to determine differences in health services quality in the PROLANIS program. Based on the gap analysis, it was found that whole dimensions were below 0-point; the CSI analysis obtained 74.45 for HT and 75.15 for DM; and the IPA analysis found that the distribution of respondents’ answers in the questionnaire were in quadrants 1 and 2. The Man–Whitney analysis was used to get the assurance aspect correlated with health service quality in DM and HT patients (p = 0.001). Health service quality in the PROLANIS program was based on five dimensions of quality was low, unless assurance dimension. The government should improve health services quality in aspects of tangibility, responsiveness, empathy, and reliability to get satisfaction among HT and DM patients in the PROLANIS program.