Despite the availability of effective vaccines for preventing common childhood infectious diseases, there is still significant disparities in access and utilization across many low- and middle-income countries (LMIC). The factors that drive these disparities are often multilevel, originating from individuals, health facilities, health systems and communities, and also multifaceted. Implementation science has emerged as a field to help address “know-do” gaps in health systems, and can play a significant role in strengthening immunization systems to understand and solve implementation barriers that limit access and uptake within their contexts. This article presents a reflexive perspective on how to position implementation research in immunization programmes to improve coverage equity. Furthermore, key points of synergy between implementation research and vaccination are highlighted, and some potential practice changes that can be applied within specific contexts were proposed. Using a human rights lens, it was concluded that the cost that is associated with implementation failure in immunization programmes is significant and unjust, and future directions for implementation research to optimize its application in practice settings have been recommended.