In Zambia, information on cost of services provided at health facilities are deficient. This study aims to contribute to fill this knowledge gap by estimating the unit costs of health services provided at different levels of health facilities. This costing exercise used cross-sectional data for the year 2016. Fourteen facilities were purposefully selected to represent different levels of health facilities and mix of characteristics. We used an accounting-based approach to calculate the unit costs of health services. Specifically, we employed the top-down approach to allocate total overhead costs incurred over to different services that were provided at the facility. Full costs of health facilities varied substantially between different levels, and even between facilities within the same level (particularly between health centres). The compositions of cost items within any facility were largely dominated by labour and material costs, each of which contributing approximately half the shares, whilst the proportion of capital costs remained small irrespective of the levels. Unit costs of outpatient services in the health centres ranged from ZMW 15 (USD 1.3) to ZMW 30 (USD 2.7) without medical consumables, while inpatient costs were between ZMW250 (USD 22.2) and ZMW 1,300 (USD 115.6) per admission and ZMW 140 (USD 12.4) to ZMW 500 (USD 44.4) per bed-day. Unit costs between services provided at the same facility exhibit fairly comparable pattern. The findings from this study provides useful information of unit costs for referencing in future studies. Further, the variations of unit costs among facilities with different characteristics provides policy relevant information for health administrators and policy makers.