The time-efficient nature of HIIT using bodyweight exercises can facilitate the application of exercise programs at home by encouraging more people to perform regular physical exercise. However, there are no studies investigating the influence of the distribution/order of exercises during HIIT training sessions using this method. The aim of the present study was to evaluate the effects of different exercise orders on training load indicators during HIIT sessions using body weight. Twenty male participants performed three 20-min sessions of HIIT using whole body exercise, consisting of 20 sets with 30 s of activity performed at maximal intensity, followed by 30 s of passive recovery. Three designs of exercise protocols were randomly performed according to the following exercise distribution: A: jumping jack, burpee, mountain climb and squat jump); B: jumping jack, mountain climb, burpee, and squat jump) and C: burpee, squat jump, jumping jack and mountain climb. No differences were found between protocols for relative heart rate, perceived exertion, and lactate concentrations. Significant differences (p < 0.001) were found for the number of movements (A:712 ± 59, B:524 ± 49, C:452 ± 65). No differences were observed for the area under curve when examining perceived exertion between protocols. However, the values for perceived recovery significantly differed (p < 0.001) between protocols (A:64 ± 19; B:52 ± 11; C:17 ± 13). Interestingly, protocol B and C induced a displeasure perception compared to protocol A. Our findings suggest that exercise distribution/order using HIIT whole body exercise promotes alterations in psychophysiological responses in HIIT using whole body exercises.