BACKGROUND: In most low- and middle-income countries, health facility regulation is fragmented, ineffective and under-resourced. The Kenyan Government piloted an innovative regulatory regime involving Joint Health Inspections (JHI) which synthesized requirements across multiple regulatory agencies; increased inspection frequency; digitized inspection tools; and introduced public display of regulatory results. The pilot significantly improved regulatory compliance. We calculated the costs of the development and implementation of the JHI pilot and modelled the costs of national scale-up in Kenya. METHODS: We calculated the economic costs of three phases: JHI checklist development, start-up activities, and first year of implementation, from the providers' perspective in three pilot counties. Data collection involved extraction from expenditure records and key informant interviews. The annualized costs of JHI were calculated by adding annualized development and start-up costs to annual implementation costs. National level scale-up costs were also modelled and compared to those of current standard inspections. RESULTS: The total economic cost of the JHI pilot was USD 1,125,600 (2017 USD), with the development phase accounting for 19%, start-up 43% and the first year of implementation 38%. The annualized economic cost was USD 519,287, equivalent to USD 206 per health facility visit and USD 311 per inspection completed. Scale up to the national level, while replacing international advisors with local staff, was estimated to cost approximately USD 4,823,728, equivalent to USD 103 per health facility visit and USD 155 per inspection completed. This compares to an estimated USD 86,997 per year (USD 113 per inspection completed) spent on a limited number of inspections prior to JHI. CONCLUSION: Information on costs is essential to consider affordability and value for money of regulatory interventions. This is the first study we are aware of costing health facility inspections in sub-Saharan Africa. It has informed debates on appropriate inspection design and potential efficiency gains. It will also serve as an important benchmark for future studies, and a key input into cost-effectiveness analyses.