BackgroundThere is a lack of consensus about how to prioritize potential implementation strategies for HIV pre-exposure prophylaxis (PrEP) delivery. We compared several prioritization methods for their agreement and pragmatism in practice in a resource-limited setting.MethodsWe engaged diverse stakeholders with clinical PrEP delivery and PrEP decision-making experience across 55 facilities in Kenya to prioritize 16 PrEP delivery strategies. We compared four strategy prioritization methods: (1) “past experience surveys” with experienced practitioners reflecting on implementation experience (N= 182); (2 and 3) “pre- and post-small-group ranking” surveys before and after group discussion (N= 44 and 40); (4) “go-zone” quadrant plots of perceived effectiveness vs feasibility. Kendall’s correlation analysis was used to compare strategy prioritization using the four methods. Additionally, participants were requested to group strategies into three bundles with up to four strategies/bundle by phone and online survey.ResultsThe strategy ranking correlation was strongest between the pre- and post-small-group rankings (Tau: 0.648;p< 0.001). There was moderate correlation between go-zone plots and post-small-group rankings (Tau: 0.363;p= 0.079) and between past-experience surveys and post-small-group rankings (Tau: 0.385;p= 0.062). For strategy bundling, participants primarily chose bundles of strategies in the order in which they were listed, reflecting option ordering bias. Neither the phone nor online approach was effective in selecting strategy bundles. Participants agreed that the strategy ranking activities conducted during the workshop were useful in prioritizing a final set of strategies.ConclusionsBoth experienced and inexperienced stakeholder participants’ strategy rankings tended to prioritize strategies perceived as feasible. Small group discussions focused on feasibility and effectiveness revealed moderately different priorities than individual rankings. The strategy bundling approach, though less time- and resource-intensive, was not effective. Future research should further compare the relative effectiveness and pragmatism of methodologies to prioritize implementation strategies.Supplementary InformationThe online version contains supplementary material available at 10.1186/s43058-023-00457-9.