Sexual violence against men in conflict and post-conflict settings is under-researched. Men’s reluctance to talk about their experiences in conflict and post-conflict settings has contributed to the subject being a difficult area of inquiry. This article describes the research design and the strategies employed by the first author, who conducted qualitative research with South Sudanese male refugees who were survivors of sexual violence and have resettled in two communities in Uganda since the onset of the 2013 South Sudan conflict. The qualitative research is a part of a mixed-method program of research for the first author’s doctoral research that focused on sexual violence perpetrated against men in conflict and post-conflict settings. Based on the learnings during the fieldwork in this complex research setting and by drawing on best practices in qualitative research, this article proposes guidelines that can assist researchers who conduct qualitative research with vulnerable populations (across multiple disciplines) on sensitive topics such as sexual violence. The guidelines include five key steps: spending time in the community before participant recruitment and data collection, fostering a trust relationship with stakeholders, using appropriate gatekeepers, making participants feel at ease throughout the research, and using the snowballing sampling technique. The key steps are interdependent and can be adapted to suit the research context. These guidelines can be useful across multiple disciplines and subject areas.