Ensuring accountability for the realization of sexual and reproductive health and rights is a human rights obligation and central tenet of strategies to improve health systems and outcomes in humanitarian settings. This pilot study explored the feasibility and acceptability of deploying human rights strategies, specifically through a participatory community-led complaints mechanism, to hold humanitarian health systems to account for the sexual and reproductive health and rights of refugee and host community women and girls in northern Uganda. Over a fifteen-month period we conducted a multi-methods exploratory study with refugee and host community rights-holders and duty-bearers using longitudinal in-depth interviews, focus groups, and secondary data document review. Deductive and inductive coding techniques were used to analyze data iteratively for content and themes. 107 sexual and reproductive health and rights related complaints and feedback were collected through the community complaints mechanism. Complaints concerned experiences of disrespect and abuse by health care workers; lack of adolescent access to sexual and reproductive health services and information; sexual and gender-based violence; and lack of access to acceptable and quality health goods and services. Participants reported an increased understanding and claiming of human rights through the intervention, acceptability of rights-based accountability strategies among humanitarian health system actors, and improved access to remedies when sexual and reproductive health rights are not respected. Findings demonstrate integrating rights-based social accountability mechanisms at the level of humanitarian response as a promising approach for strengthening and holding humanitarian health systems accountable for the sexual and reproductive health and rights of women and girls affected by humanitarian situations.