Performance-based financing (PBF) is a mechanism to improve the quality and the utilisation of health benefit packages. There is a dearth of economic evaluations of PBF in the 'real world'. Afghanistan implemented PBF between 2010 and 2015 and evaluated the programme using a pragmatic cluster-randomised control trial. We conducted a cost-effectiveness analysis of the PBF programme in Afghanistan, compared with the standard of care, from the provider payer's perspective. The incremental cost-effectiveness ratio of PBF compared with the standard of care was US$1242 per disability-adjusted life year averted; not cost-effective when compared with an opportunity cost threshold of US$349. Incentive payments were the main contributor to PBF financial cost (70%) followed by data verification (23%), staff time (5%) and administration (2%). The unit cost per case of antenatal care (ANC), skilled birth attendance (SBA) and postnatal care (PNC) services in the standard of care was US$0.96 (95% CI 0.92-1.0), US$4.8 (95% CI 4.1-6.3) and US$1.3 (95% CI 1.2-1.4), respectively, whereas the cost of ANC, SBA and PNC services per case in PBF areas were US$4.72 (95% CI 4.68-5.7), US$48.5 (95% CI 48.0-52.5) and US$5.4 (95% CI 5.1-5.9), respectively. To conclude, our study found that PBF, as implemented in the Afghan context, was not the best use of funds to strengthen the delivery of maternal and child health services. The cost-effectiveness of alternative PBF designs needs to be appraised before using PBF at scale to support health benefit packages. PBF needs to be considered in the context of funding the range of constraints that inhibit health service performance improvement.