Abstract Background Primary care clinics play a crucial role in community health promotion by facilitating early disease detection and management. The number of these clinics in Gwangju Metropolitan City increased from 931 in 2000 to 2,400 in 2022, but this growth was not evenly distributed within the city. This study aims to examine the spatial inequalities in the distribution of clinics in Gwangju Metropolitan City. Methods This study utilized local administrative licensing data on medical institutions classified as clinics. To estimate healthcare resource imbalances, Lorenz curves and Gini indices for the number of clinics per 100,000 individuals and per square kilometer were calculated by district. Results The number of primary care clinics per 1,000 individuals or per square kilometer was highest in Dong-gu and Seo-gu, while Gwangsan-gu had relatively fewer facilities. In particular, Buk-gu, Seo-gu, and Nam-gu had more than 40% of areas with a high number of healthcare facilities relative to population or area, whereas less than 50% of Gwangsan-gu fell into the lower tier in these categories. The Gini index, used to measure the geographical inequality of healthcare facility distribution, showed a slight improvement from 2000 to 2023. However, Seo-gu and Buk-gu exhibited different trends compared to other districts. Conclusions Geographical disparities in the distribution of primary care clinics in Gwangju Metropolitan City have slightly improved since 2000, but show different patterns by district. Addressing healthcare imbalances is essential for enhancing health equity, requiring multifaceted efforts to mitigate disparities and improve medical service accessibility in underserved areas. Key messages • Significant disparities exist in the distribution of primary care clinics across Gwangju, with higher densities in Dong-gu and Seo-gu, and fewer facilities in Gwangsan-gu. • The Gini index for clinic distribution has improved since 2000, but disparities remain, particularly in Seo-gu and Buk-gu. Continued efforts are essential to reduce healthcare inequalities further.