Humanitarian assistance standards require specific attention to address the reproductive health (RH) needs of conflict-affected populations. Despite these internationally recognised standards, access to RH services is still often compromised in war. We assessed the effectiveness of our programme in northern Uganda to provide family planning (FP) services through mobile outreach and public health centre strengthening. Baseline (n=905) and endline (n=873) cross-sectional surveys using a multistage cluster sampling design were conducted in the catchment areas of four public health centres in 2007 and 2010. Current use of any modern FP method increased from 7.1% to 22.6% (adjusted odds ratio [OR] 3.34 [95% confidence interval (CI) 2.27–4.92]); current use of long-acting and permanent methods increased from 1.2% to 9.8% (adjusted OR 9.45 [95%CI 3.99–22.39]). The proportion of women with unmet need for FP decreased from 52.1% to 35.7%. This study demonstrates that when comprehensive FP services are provided among conflict-affected populations, women will choose to use them. The combination of mobile teams and health systems strengthening can make a full range of methods quickly available while supporting the health system to continue to provide those services in challenging and resource-constrained settings.