Knowing the cost of health care services is a prerequisite for evidence-based management and decision making. However, only limited costing data is available in many low- and middle-income countries. With a substantially increasing number of facility-based births in Cambodia, costing data for efficient and fair resource allocation is required. This paper evaluates the costs for cesarean section (CS) at a public and a Non-Governmental (NGO) hospital in Cambodia in the year 2018. We performed a full and a marginal cost analysis, i.e., we developed a cost function and calculated the respective unit costs from the provider’s perspective. We distinguished fixed, step-fixed, and variable costs and followed an activity-based costing approach. The processes were determined by personal observation of CS-patients and all procedures; the resource consumption was calculated based on the existing accounting documentation, observations, and time-studies. Afterwards, we did a comparative analysis between the two hospitals and performed a sensitivity analysis, i.e., parameters were changed to cater for uncertainty. The public hospital performed 54 monthly CS with an average length of stay (ALOS) of 7.4 days, compared to 18 monthly CS with an ALOS of 3.4 days at the NGO hospital. Staff members at the NGO hospital invest more time per patient. The cost per CS at the current patient numbers is US$470.03 at the public and US$683.23 at the NGO hospital. However, the unit cost at the NGO hospital would be less than at the public hospital if the patient numbers were the same. The study provides detailed costing data to inform decisionmakers and can be seen as a steppingstone for further costing exercises.