Abstract Background The primary aim of this study was to examine the associations of normal weight obesity (NWO) with physical fitness in Chinese university students. As a secondary aim, we assessed whether possible differences in physical fitness between students classified as NWO and normal weight non-obese (NWNO) were mediated by skeletal muscles mass. Methods A total of 383 students (205 males and 178 females, aged 18–24 years) from two universities volunteered to participate in this study. Body height and weight were measured by standard procedures and body composition was assessed by bio-impedance analysis (InBody 720). NWO was defined by a BMI of 18.5–23.9 kg/m2 and a body fat percentage of > 20% or > 30% in male and female students, respectively. Physical fitness was measured using a 10-min intermittent endurance running test (Andersen test), countermovement jumps (CMJ) and a 5 × 5 m shuttle run test (5mSR). The level of leisure time physical activity (PA) was assessed by a questionnaire. Results 13.7% of male and 27.5% of female students were classified as NWO. Compared to NWNO, students classified as NWO showed a significantly poorer performance in the Andersen test (males: 1146 ± 70 m vs. 1046 ± 95 m, females: 968 ± 61 m vs. 907 ± 67 m, p