The relationship between fat-free mass (FFM) and excess post-exercise oxygen consumption (EPOC) has not been well researched because of the relatively small number of subjects studied. This study investigated the effects of FFM on EPOC and EPOC/maximum oxygen consumption. 250 Japanese male athletes between 16 and 21 years old from Nagasaki prefecture had their EPOC measured up to 40 minutes after short-duration exhaustive exercise. The value was named as EPOC_{40 min}. The proportions of EPOC up to 1, 3, 6, 10, and 25 minutes to EPOC_{40 min} were calculated and named as P1, P3, P6, P10, and P25, respectively. Body size and composition, VO₂max and resting metabolic rate (RMR) were also measured. Mean EPOC_{40 min} was 9.04 L or 158 ml/kg FFM. EPOC_{40 min} was related to FFM (r=0.55, p <0.001) and VO₂max (r=0.37, p <0.001). The ratio of EPOC_{40 min} to VO₂max was related to FFM (r=0.28, p <0.001). P1, P3, P6, P10, and P25 were negatively related to EPOC_{40 min}/FFM, EPOC_{40 min}/VO₂max, and FFM. Athletes who had larger FFM had larger EPOC40_{40 min} and EPOC40_{40 min}/VO₂max, and smaller P1, P3, P10, and P25.