Globally, it is estimated that at least one out of every three women experiences violence by an intimate partner and/or non-partner throughout their lifetime. Women and girls are at even higher risk of violence in conflict and humanitarian crises. Although effort has expanded to build rigorous evidence and research on violence against women and girls (VAWG) among conflict-affected populations, methodological and ethical challenges remain. Basic ethical research practices are more challenging in conflict-affected populations and therefore require supplementary protections. While it is important to follow international ethical guidelines, in practice it is sometimes difficult depending on the setting. The aim of this paper is to present the main ethical challenges that occur when conducting research on VAWG in conflict and humanitarian settings, as well as potential strategies to address these challenges, based on a recent study carried out in South Sudan in 2016.