Background: The Afghan health system is unique in that primary healthcare is delivered by donor-funded implementing partners, not the government. Given the wide range of implementers providing the basic package of health services, there may exist performance differences in primary healthcare. This study assessed the relative efficiency of different levels of primary healthcare services and explored its determinants in Afghanistan. Method: Data on personnel and capital expenditure (inputs) and the number of facility visits for six primary healthcare services (outputs) were obtained from national health information databases for 1,263 healthcare facilities in 31 provinces. Data envelopment analysis was used to assess the relative efficiency of three levels of primary healthcare facilities (comprehensive, basic, and sub health centers). Bivariate analysis was conducted to assess the correlation of various elements with efficiency scores. Regression models were used to identify potential factors associated with efficiency scores at the health facility level. Results: The average efficiency score of health facilities was 0.74, when pooling all 1,263 health facilities, with 102 health facilities (8.1%) having efficiency scores of 1 (100% efficient). The lowest quintile of health facilities had an average efficiency score of 0.36 while the highest quintile had a score of 0.96. On average, efficiency scores of comprehensive health centers were higher than basic and sub health centers by 0.108 and .071 respectively. In addition, the difference between efficiency scores of facilities in the highest and lowest quintiles was highest in facilities that offer fewer services, so that they have the largest room for improvement. Conclusions: Our findings show that public health facilities in Afghanistan that provide more comprehensive primary health services, use their resources more efficiently, and that smaller facilities have more room for improvement. A more integrated delivery model would help improve the efficiency in providing primary healthcare in Afghanistan.