Men who have sex with men (MSM) in Malaysia are disproportionately affected by HIV. As pre-exposure prophylaxis (PrEP) is being introduced, we assessed population-based PrEP delivery preferences among MSM in Malaysia. We conducted a discrete choice experiment through an online survey among 718 MSM. The survey included 14 choice tasks presenting experimentally varied combinations of five attributes related to PrEP delivery (i.e., cost, dosing strategy, clinician interaction strategy, dispensing venue, and burden of visits to start PrEP). We used latent class analysis and Hierarchical Bayesian modeling to generate the relative importance of each attribute and preference across six possible PrEP delivery programs. PrEP dosing, followed by cost, was the most important attribute. The participants were clustered into five preference groups. Two groups (n = 290) most commonly preferred on-demand, while the other three preferred injectable PrEP. One group (n = 188) almost exclusively considered cost in their decision-making, and the smallest group (n = 86) was substantially less interested in PrEP for reasons unrelated to access. In simulated scenarios, PrEP initiation rates varied by the type of program available to 55·0% of MSM. Successful PrEP uptake among Malaysian MSM requires expanding beyond daily oral PrEP to on-demand and long-acting injectable PrEP, especially at affordable cost.