As a result of new global priorities, there is a growing need for high-quality evaluations of gender-integrated health programmes. This systematic review examined 99 peer-reviewed articles on evaluations of gender-integrated (accommodating and transformative) health programmes with regard to their theory of change (ToC), study design, gender integration in data collection, analysis, and gender measures used. Half of the evaluations explicitly described a ToC or conceptual framework (n=50) that guided strategies for their interventions. Over half (61%) of the evaluations used quantitative methods exclusively; 11% used qualitative methods exclusively; and 28% used mixed methods. Qualitative methods were not commonly detailed. Evaluations of transformative interventions were less likely than those of accommodating interventions to employ randomised control trials. Two-thirds of the reviewed evaluations reported including at least one specific gender-related outcome (n=18 accommodating,n=44 transformative). To strengthen evaluations of gender-integrated programmes, we recommend use of ToCs, explicitly including gender in the ToC, use of gender-sensitive measures, mixed-method designs, in-depth descriptions of qualitative methods, and attention to gender-related factors in data collection logistics. We also recommend further research to develop valid and reliable gender measures that are globally relevant.