Physical fitness is an important determinant of work ability and is closely associated with work quality, productivity, and overall job satisfaction. In hospital settings, where employees are exposed to sustained physical and psychological demands, impaired physical fitness compromise occupational performance and long-term health. However, the relative contributions of physical, mental, and subjective health factors to physical fitness risk among hospital employees remain unclear.This study aimed to examine independent factors associated with a high risk of physical fitness impairment among hospital employees, with a particular focus on whether these associations differ according to work tenure.This cross-sectional study stratified participants by work tenure into those with less than 10 years and those with ≥10 years of employment. Binary logistic regression analyses were performed to identify independent predictors of high risk of physical fitness impairment, adjusting for potential confounders including age, sex, BMI, Waist-to-Hip Ratio (WHR), skeletal muscle mass, and health-related quality of life domains derived from the SF-36 questionnaire (Physical Component Summary [PCS], Mental Component Summary [MCS], and General Health [GH]). Tenure-stratified models were further conducted.A total of 365 hospital employees were enrolled. In tenure-stratified analyses, subjective general health (GH) was independently associated with a high risk of physical fitness impairment among employees with ≥10 years of tenure (OR 0.27, 95% CI 0.12–0.62; p = 0.002), whereas PCS and MCS were not significantly associated with physical fitness risk. In this group, higher BMI and WHR were positively associated with physical fitness impairment, while greater skeletal muscle mass and sex were inversely associated with physical fitness risk. In contrast, no significant independent predictors were identified among employees with less than 10 years of tenure.Among long-tenured hospital employees, subjective general health emerged as a key predictor of physical fitness impairment, outperforming conventional physical and mental health scores. These findings suggest that subjective health perception may capture cumulative occupational and metabolic burdens that are not reflected by traditional health metrics.Our results indicate that tenure-specific strategies incorporating subjective health assessment may enhance the effectiveness of workplace physical fitness and health promotion programs.