Civil–military relationships are necessary in humanitarian emergencies but, if poorly managed, may be detrimental to the efforts of humanitarian organizations. Awareness of guidelines and understanding of risks relating to the relationship among deployed military personnel have not been evaluated.

Fifty-five military and 12 humanitarian healthcare workers in South Sudan completed questionnaires covering experience, training and role, agreement with statements about the deployment, and free text comments.

Both cohorts were equally aware of current guidance. Eight themes defined the relationship. There was disagreement about the benefit to the South Sudanese people of the military deployment, and whether military service was compatible with beneficial health impacts. Two key obstacles to the relationship and 3 areas the relationship could be developed were identified.

This study shows that United Kingdom military personnel are effectively trained and understand the constraints on the civil–military relationship. Seven themes in common between the groups describe the relationship. Current guidance could be adapted to allow a different relationship for healthcare workers.