The adverse effects of hard contact lenses (HCL) on the corneal endothelium have been studied in the short term; however, long-term effects remain still unclear. In this study, we analyzed the effect of long-term HCL use on corneal endothelial cell density (ECD) and morphology in healthy Japanese individuals. This cross-sectional observational study included individuals using HCL for refractive errors examined at a single specialty eye hospital. Patient age, duration of HCL usage, ECD, coefficient of variation of the cell area (CV), and rate of appearance of hexagonal cells (6A) obtained via non-contact specular microscopy were assessed. We analyzed 8604 eyes (mean age: 35.6 ± 10.0 years, 837 males, 3465 females). The mean duration of HCL usage was 14.7 ± 9.1 (range, 1–50) years. Multivariate analysis revealed that ECD significantly correlated with age (P< 0.001) but not with duration of usage; however, CV and 6A significantly correlated with both factors (P< 0.001). Univariate analysis revealed that CV and 6A correlated with duration of usage (all,P< 0.001). According to our results, CV and 6A correlated with the duration of HCL usage in ophthalmologically healthy Japanese individuals. Therefore, it is important to monitor corneal endothelial morphology in long-term HCL wearers.