Objectives The purpose of this study was to investigate excess postexercise oxygen consumption (EPOC) induced by isocaloric bouts of continuous and intermittent running and cycling exercise. Design This was a counterbalanced randomized cross-over study. Methods Ten healthy men, aged 23–34 yr, performed six bouts of exercise: (a) two maximal cardiopulmonary exercise tests for running and cycling to determine exercise modality-specific peak oxygen uptake (VO2peak); and (b) four isocaloric exercise bouts (two continuous bouts expending 400 kcal and two intermittent bouts split into 2 × 200 kcal) performed at 75% of the running and cycling oxygen uptake reserve. Exercise bouts were separated by 72 h and performed in a randomized, counter-balanced order. The VO2 was monitored for 60-min postexercise and for 60-min during a control non-exercise day. Results The VO2 was significantly greater in all exercise conditions compared to the control session (P < 0.001). The combined magnitude of the EPOC from the two intermittent bouts was significantly greater than that of the continuous cycling (mean difference = 3.5 L, P = 0.001) and running (mean difference = 6.4 L, P < 0.001). The exercise modality had a significant effect on net EPOC, where running elicited a higher net EPOC than cycling (mean difference = 2.2 L, P < 0.001). Conclusions Intermittent exercise increased the EPOC compared to a continuous exercise bout of equivalent energy expenditure. Furthermore, the magnitude of EPOC was influenced by exercise modality, with the greatest EPOC occurring with isocaloric exercise involving larger muscle mass (i.e., treadmill running vs. cycling).