This study aimed to investigate the impact of percent body fat (%BF) on muscle damage after high-intensity eccentric exercise. Thirty healthy male undergraduates (mean age: 22.0 ± 2 years, height: 176.9 ± 5 cm, weight: 75.8 ± 11.6 kg) participated in this study, and they were classified according to their %BF into a high %fat group (HFG, ≥20%, n = 15) and a low %fat group (LFG, ≤15%, n = 15). For eccentric exercise, two sets of 25 reps were performed on a modified preacher curl machine using the elbow flexor muscle. Maximal isometric strength, muscle soreness (passive and active), creatine kinase (CK), and myoglobin (Mb) were measured as indices of muscle damage. The data were analyzed with repeated measures ANOVA. The results show that there is a significant group–time interaction for both CK and Mb after eccentric exercise (p = 0.007, p = 0.015, respectively), with a greater increase in the HFG than in the LFG. However, there was no significant group–time interaction for maximal isometric strength and muscle soreness (passive and active) (p > 0.05). These results suggest that %BF is a factor that alters the muscle damage indices CK and Mb, which indicate membrane disruption, after eccentric exercise.