Objectives: The objective of this study was to investigate the factors associated with website operation among medical facilities.Methods: A cross-sectional study design was employed to investigate 1,519 hospitals, 33,043 medical clinics (MCs), and 18,240 dental clinics (DCs) as of 2020. The main outcome variable was analyzed according to technological, organizational, and environmental factors.Results: The percentages of small hospitals, MCs, and DCs with websites were 26.4%, 9.0%, and 6.6%, respectively. For small hospitals, the nearby presence of a subway station (odds ratio [OR] = 2.772; 95% confidence interval [CI], 1.973–3.892; p < 0.0001) was the only factor significantly associated with website operation status. Among medical and dental clinics, the percentage of specialists—MCs (OR = 1.002; 95% CI, 1.000–1.004; <i>p</i> = 0.0175) and DCs (OR = 1.002; 95% CI, 1.001–1.004; <i>p</i> = 0.0061), the nearby presence of a subway station—MCs (OR = 2.954; 95% CI, 2.613–3.339; <i>p</i> < 0.0001) and DCs (OR = 3.444; 95% CI, 2.945–4.028; <i>p</i> < 0.0001), and the number of clinics in the local area—MCs (OR = 1.029; 95% CI, 1.026–1.031; <i>p</i> < 0.0001) and DCs (OR = 1.080; 95% CI, 1.066–1.093; <i>p</i> < 0.0001)—were significantly associated with website operation.Conclusions: Clinics are critically affected by internal and external factors regarding website operation relative to small hospitals. Healthcare policymakers involved with information technologies may need to pay attention to those factors associated with website dispersion among small clinics.