This paper reports on an investigation into the effects of gender mainstreaming efforts on the institutions that deliver and support rural transport infrastructure and services in Kenya. It comes at a time when the nation is implementing robust policies, supported by enabling legislative and institutional frameworks for gender mainstreaming as required by the Constitution of Kenya 2010. A multi-level case study was conducted at national and county levels where many institutions were surveyed. Qualitative and quantitative data were collected, covering gender analysis in staffing, decision-making and procurement for a sample of rural transport institutions. Results show that gender mainstreaming efforts have transformed rural transport institutions towards gender-responsive staffing, human-resource practices, budgeting, procurement and implementation of transport-related works. However, achieving the constitutional two-thirds affirmative action policy in staffing remains a challenge, more so in technical and decision-making bodies. The study found that the meaning and purpose of gender mainstreaming is not sufficiently understood by the majority of transport sector institutions. Additionally, gender-disaggregated data are neither readily available nor applied to rural transport programming and implementation. A change of strategy and long-term progressive efforts are required to realise gender equity in rural transport institutions in Kenya and beyond.