Abstract Background Electronic health (eHealth) interventions are promising in HIV and sexually transmitted infections (STIs) prevention among men who have sex with men (MSM), given a high rate of the Internet use in this population. This study determined the preferences for eHealth interventions to prevent HIV and STIs among MSM in Hanoi, Vietnam to guide the development of future eHealth interventions. Methods Five focus group discussions (FGD) were conducted with 35 MSM recruited by purposive sampling in January 2018 in Hanoi, Vietnam. The FGDs addressed attitudes towards the feasibility and uptake of HIV/STI interventions via online modalities such as smartphone applications (apps, social network sites, or emails); preferences and concerns regarding an online HIV/STI intervention. FGDs were audio-recorded and transcribed verbatim. Content analysis was used to determine themes. Results MSM reported that they commonly searched for information regarding HIV/STI and sexual health on Facebook and a variety of mobile apps. They perceived a lack of reliable online sources, a high need, and interest for an online intervention. Most of them preferred short and concise messages without perceived sensitive words such as “HIV” or “STI”. Diversity of online modalities were preferred with information from credible sources about HIV/STI symptoms, testing and treatment, safe sex practices and testing locations with a focus on safe MSM-friendly clinics. Concerns about the need to trust the organization behind the online information and interventions, and the importance of confidentiality when participating in online interventions were raised. Conclusion High acceptance and perceived need for an online HIV/STI intervention were reported. The importance of establishing trust within the MSM community as a reliable source of information was emphasized, as well as the importance of confidentiality.