Studies on the application of complex adaptive systems (CAS) framework to describe variations in free healthcare policies during implementation are limited. This study uses a CAS framework to explore interactions among actors and to explain how specific characteristics of CAS framework change in institutional designs of a Free Maternal and Child Healthcare Program (FMCHP) in Nigeria. A qualitative, case study approach was used to collect data on variations in features of FMCHP from policymakers (n = 16) and providers (n = 16) selected by purposeful sampling from the Ministry of Health and two health districts in Enugu State based on their posts in FMCHP, using semi-structured interview. Additional qualitative data were collected through document review. Main actors, their roles, incentives, and power were identified. Data were analyzed using thematic analysis guided by a CAS framework. Six core features of FMCHP changed during implementation, namely, revenue collection, the role of Ministry of Health, the role of the state teaching hospital, introduction of evidence of tax payment, provider payment process, and establishment of a Financial Monitoring Committee. Formal rules alone did not guarantee consistency and stability of policies. Power imbalances, coordination, and cooperation among actors affected fidelity of policy implementation. The CAS phenomena associated with these changes include path dependence, feedback, lever points, emergent behaviors, and phase transition. Managing changes in free healthcare policies requires recognizing the power shifts, nonlinearity of outcomes, unpredictable consequences and feedbacks, and addressing the context, adaptive behavior, and network of actors.