This case study examines whether health system reconstruction in northern Uganda has promoted equality and created a health system that is gender equitable. Measuring the health system against the World Health Organization’s six health system building blocks, the case study highlights that northern Uganda needs a post-conflict recovery plan which is sensitive to gender concerns. What little has been done for the survivors of gender-based violence has not been linked to overall health systems strengthening: this constitutes a missed opportunity. Gender equitable finding mechanisms and action to consider the health workforce from a gender perspective are identified as key.