Implementation science (IS) uses systematic methods to close gaps between research and practice by identifying and addressing barriers to implementation of evidence-based interventions (EBIs). To reach UNAIDS HIV targets, IS can support programs to reach vulnerable populations and achieve sustainability. We studied the application of IS methods in 36 study protocols that were part of the Adolescent HIV Prevention and Treatment Implementation Science Alliance (AHISA). Protocols focused on youth, caregivers, or healthcare workers in high HIV-burden African countries and evaluated medication, clinical and behavioral/social EBIs. All studies measured clinical outcomes and implementation science outcomes; most focused on early implementation outcomes of acceptability (81%), reach (47%), and feasibility (44%). Only 53% used an implementation science framework/theory. Most studies (72%) evaluated implementation strategies. Some developed and tested strategies, while others adapted an EBI/strategy. Harmonizing IS approaches allows cross study learning and optimization of delivery of EBIs and could support attainment of HIV goals.