The security of civilians in contemporary conflicts continues to tragically elude humanitarians. Scholars attribute this crisis in protection to macro-structural deficiencies, such as the failure of states to comply with international conventions and norms and the inability of international institutions to successfully reduce violence by warring parties. While offering important insights into humanitarianism and its limits, this scholarship overlooks the potential of endogenous sources of protection – the agency of civilians. On the basis of a case study of northern Uganda, we identify and discuss several civilian self-protection strategies, including (a) attempts to appear neutral, (b) avoidance and (c) accommodation of armed actors, and argue that each of these is shaped by access to local knowledge and networks. We illustrate how forced displacement of civilians to ‘protected villages’ limited access to local knowledge and, in turn, the options available to civilians in terms of self-protection. Analyses of the intersections of aid and civilian agency in conflict zones would afford scholars of humanitarianism greater explanatory insight into questions of civilian protection. The findings from our case study also suggest ways in which aid agencies could adopt protection strategies that empower – or at least do not obstruct – the often-successful protection strategies adopted by civilians.