IntroductionKenya reported its first COVID-19 case on 13 March 2020. Pandemic-driven health system changes followed and unforeseen societal, economic and health effects reported. This protocol aims to describe the methods used to identify the gender equality and health equity gaps and possible disproportional health and socioeconomic impacts experienced by paid and unpaid (community health volunteer) female healthcare providers in Kilifi and Mombasa Counties, Kenya during the COVID-19 pandemic.Methods and analysisParticipatory mixed methods framed by gender analysis and human-centred design will be used. Research implementation will follow four of the five phases of the human-centred design approach. Community research advisory groups and local advisory boards will be established to ensure integration and the sustainability of participatory research design.Ethics and disseminationEthical approval was obtained from the Institutional Scientific and Ethics Review Committee at the Aga Khan University and the University of Manitoba.This study will generate evidence on root cultural, structural, socioeconomic and political factors that perpetuate gender inequities and female disadvantage in the paid and unpaid health sectors. It will also identify evidence-based policy options for future safeguarding of the unpaid and paid female health workforce during emergency preparedness, response and recovery periods.