Background: Public health literature is replete with evidence on individual and interpersonal indicators of modern contraceptive use. There is, however, limited knowledge regarding healthcare system indicators of modern contraceptive use. This study assessed how the healthcare system influences use of modern contraceptive among women in Ghana, Kenya, and two large population states in Nigeria. Methods: This study used data from Phase 1 of the Performance Monitoring and Accountability 2020. The analytical sample was limited to women with a need for contraception, defined as women of reproductive age (15 to 49 years) who wish to delay or limit childbirth. Therefore, this analysis consisted of 1066, 1285, and 1955 women from Nigeria, Ghana, and Kenya respectively. Indicators of healthcare assessed include user-fees, visit by health worker, type of health facility, multiple perinatal services, adolescent reproductive healthcare, density of healthcare workers, and regularity of contraceptive services. All analyses were conducted with SAS (9.4), with statistical significance set at p < 5%. Results: The prevalence of modern contraceptive was 22.7, 33.2, and 68.9% in Nigeria, Ghana, and Kenya respectively. The odds of modern contraceptive use were higher among Nigerian women who lived within areas that provide adolescent reproductive healthcare (OR = 2.05; 95% C.I. = 1.05-3.99) and Kenyan women residing in locales with polyclinic or hospitals (OR = 1.91; 1.27-2.88). Also, the odds of contraceptive use were higher among Kenyan women who lived in areas with user-fee for contraceptive services (OR = 1.40; 1.07-1.85), but lower among Ghanaian women residing in such areas (OR = 0.46; 0.23-0.92). Lastly, the odds of modern contraceptive use were higher among women visited by a health-worker visit among women in Ghana (OR = 1.63; 1.11-2.42) and Nigeria (OR = 2.97; 1.56-5.67) than those without a visit. Conclusion: This study found an association between country-specific indicators of healthcare and modern contraceptive use. Evidence from this study can inform policy makers, health workers, and healthcare organizations on specific healthcare factors to target in meeting the need for contraception in Ghana, Kenya, and Nigeria.