Large-scale epidemics in resource-constrained settings disrupt delivery of core health services, such as routine immunization. Rebuilding and strengthening routine immunization programs following epidemics is an essential step toward improving vaccine equity and averting future outbreaks. We performed a comparative case study analysis of routine immunization program recovery in Liberia and Haiti following the 2014–16 West Africa Ebola epidemic and 2010s cholera epidemic, respectively. First, we triangulated data between the peer-reviewed and grey literature; in-depth key informant interviews with subject matter experts; and quantitative metrics of population health and health system functioning. We used these data to construct thick descriptive narratives for each case. Finally, we performed a cross-case comparison by applying a thematic matrix based on the Essential Public Health Services framework to each case narrative. In Liberia, post-Ebola routine immunization coverage surpassed pre-epidemic levels, a feat attributable to investments in surveillance, comprehensive risk communication, robust political support for and leadership around immunization, and strong public-sector recovery planning. Recovery efforts in Haiti were fragmented across a broad range of non-governmental agencies. Limitations in funding, workforce development, and community engagement further impeded vaccine uptake. Consequently, Haiti reported significant disparities in subnational immunization coverage following the epidemic. This study suggests that embedding in-country expertise within outbreak response structures, respecting governmental autonomy, aligning post-epidemic recovery plans and policies, and integrating outbreak response assets into robust systems of primary care contribute to higher, more equitable levels of routine immunization coverage in resource-constrained settings recovering from epidemics.