Healthcare workers (HCWs) face a high risk of infection during pandemics or public health emergencies as demonstrated in the ongoing COVID-19 pandemic. Understanding how governments respond can inform public health control measures and support health system functioning. An economic impact analysis examining HCW COVID-19 infections in Kenya and three other countries estimated that the total economic costs related to HCW COVID-19 infections costs and deaths in Kenya were US$113.2 million (range US$35.8-US$246.1). We examined the governance arrangements for and implementation of HCW protection during the COVID-19 pandemic in Kenya between March 2020 and March 2021. We conducted a scoping review of 44 policy and legislative documents and reports on HCW protection and 22 media articles. We adopted the transparency, accountability, participation, integrity and capacity (TAPIC) governance framework to analyse and summarize our findings into policy gaps and implementation challenges. Policy design gaps included inadequate provisions for emerging threats, inconsistencies with the devolved context and inadequate structures to monitor, inform and respond to HCW COVID-19 infections. Implementation challenges were attributed to inadequate quantity and quality of PPE, difficulty in accessing medical care for HCWs, delays in HCW remuneration, insufficient infection prevention and control measures, the top-down application of plans, difficulties in working in a decentralized context, and pre-existing public finance management (PFM) bottlenecks. Implementation of HCW protection during the COVID-19 pandemic and beyond could leverage the revamping of current legislation on labour relations to reflect devolved governance and develop a broader and long-term approach to occupational health and safety implementation that considers all HCWs. Improvements in PFM arrangements coupled with increased investment in the health sector and attention to efficient use of resources will also impact positively on HCW protection.