Introduction: The moderate-intensity continuous exercise (MICE) is aiming to decrease the risks of atherosclerosis and cardiovascular disease. Recently, low-volume high-intensity interval exercise (HIIE) has been considered as a time-efficient approach to prevent these chronic diseases in adults. High-fat meal (HFM) may affect inflammatory and brain-derived neurotrophic factor (BDNF); however, the effects of different exercise and high-fat meal intervention on interleukin-6 (IL-6) and BDNF is unclear. The purpose of this study was to compare the effects of MICE and HIIE on IL-6 and BDNF followed the high-fat meal. Methods: Thirty-six males were randomly assigned to three trials which exercising in the evening: a HIIE (10 × 1 min sprints at 85% of maximal oxygen uptake with a 2 min resting interval between intense exercises), a MICE (aerobic exercise at 65% of maximal oxygen uptake for 50-min), and a control (CON). The next morning after exercising, participants consumed a HFM of 13 kcal/kg body mass after a 12 hr overnight fast. Blood draws were performed immediately before and after exercising on day 1, before HFM and then hourly until 4 hr on day 2. Results: At baseline, there was no difference between three trials for IL-6 and BDNF levels (P > 0.05). There was evidence of acute increase in IL-6 concentration in response to the HIIE (P = 0.02) and MICE (P = 0.00) compared to CON after exercise, but no significant differences observed at other time points among HIIE, MICE, and CON (P > 0.05). The area under curve (AUC) of IL-6 was significantly higher in MICE than those in HIIE and CON from pre- to post-exercise (P = 0.00–0.03), and MICE and HIIE had higher IL-6 AUC compared with CON from post-exercise to pre-meal (P = 0.00–0.05). BDNF increased after exercise in HIIE and MICE compared with CON (P = 0.01), but HIIE and MICE were not different. No significant difference in BDNF after HFM among three trials (P > 0.05). During 12 hr post-exercise, BDNF AUC was increased by 23% and 21% in HIIE and MICE compared with CON respectively, but HIIE did reach a significantly different (P = 0.05) rather than MICE (P = 0.08). Conclusion: Acute HIIE and MICE equally increased IL-6 and BDNF concentrations response to the exercise, but only HIIE could maintain a longer and higher BDNF level after HIIE. However, the effect of the BDNF level attenuated gradually after ingestion of HFM in the morning after acute exercise in the evening.