Primary health care (PHC) is a universally accepted key strategy to achieve universal health coverage (UHC) and Sustainable Development Goal 3 (SDG 3) due to its potential to produce a range of economic benefits through improved health outcomes, health quality, and health system efficiency. However, little evidence exists about the cost efficiency of primary health care facilities (PHCFs) in Sub-Saharan Africa. This study evaluates the cost efficiency of two main types of PHCFs in Ghana that are at the forefront of delivering PHC services to a greater proportion of the population: Community Health Centers (HCs) and Community-Based Health Planning Services (CHPS) compounds. The dataset we used for this study included 39 HCs and 55 CHPS facilities. Furthermore, it examines the factors that influence the cost efficiency of these facilities. The study applies the stochastic frontier analysis (SFA) technique to panel data. The estimated cost efficiency for HCs and CHPS is 61.6% and 85.8%, respectively. The study further revealed that facility size, medical staff density, and facility age are the main factors that explain the differences in the cost efficiency of PHCFs in Ghana. The study's policy recommendation is that the Ghana Health Service should consider utilizing modern technology such as telehealth and telemedicine to enhance access to PHC services for people living in hard-to-reach and densely populated communities. This strategic approach can significantly contribute to improving the cost-efficiency of PHCFs.