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Background: Ghana introduced capitation payment method in 2012 but was faced with resistance for its perceived poor quality of care. This paper assesses National Health Insurance Scheme subscribers and care providers’ perception of quality of care under the capitation payment method. Methods: This is a cross-sectional survey of subscribers and care providers perception of quality of care in three administrative regions of Ghana using a 5-point Likert scale for the assessment based on a set of quality of care measures. We performed descriptive analysis to determine average perception of quality of care scores for each of the measures used. Bivariate and multivariate analyses were also performed to examine relationships between respondent’s characteristics and their perception of quality of care. Results: In general, subscribers expressed positive perception about the quality of care though subscribers in Ashanti were less positive compared to those in the Central region. A chi-square analysis, however, showed significant differences in subscribers’ perception of quality of care by occupation (p = 0.002), region (p = 0.007) length of NHIS membership (p = 0.006), and age (p = 0.014). Multivariate logistic regression analysis also showed that different factors, other than region of residence, were significantly associated with perceived good quality of care. Analysis of health care providers’ responses also showed significant differences in their perception of quality of care by region (p = 0.001). Multivariate logistic model showed that health care providers in the Volta region (OR = 0.14, 95% CI: 0.03–0.58) were significantly less likely to perceive quality of care as good compared to those in the Ashanti region. Conclusion: Subscribers and care providers across the three regions have relatively good perception of the quality of health care in general though subscribers in Ashanti were less positive than those in the Central region. It is, therefore, plausible that capitation payment may have influenced the relatively low perception of quality of care in the Ashanti region. [ABSTRACT FROM AUTHOR]