Introduction: To achieve universal health coverage, Kenya will need to mobilize additional resources for the health sector. Efficiency gains are a potential pathway to unlocking additional resources. Given that corruption has been cited as a key cause of inefficiency in the health sector, we examined the influence of corruption on the efficiency of Kenyan county health systems. Methods We conducted a qualitative case study of two Kenyan counties. We developed a conceptual framework based on a literature review to guide the development of tools and analyses. We collected qualitative data through in-depth interviews (n = 26) with county-, sub-county-, and health facility-level respondents across the two counties. We analyzed the data collected using the framework approach. Findings Corrupt practices reported in the case study counties included non-merit-based recruitment and training of health workers; supply of substandard goods, equipment, and infrastructure; theft, embezzlement, and misuse of public funds and property; and informal payments. These practices were perceived to negatively impact health sector efficiency by leading to a direct loss of health sector resources, an increase in operational costs, poor quality of care, reduced staff motivation and productivity, and reduced access to healthcare services. Conclusion The efficiency of county health systems could be enhanced by implementing anti-corruption strategies to tackle identified corrupt practices.