BackgroundIn high-intensity interval training (HIIT), the rest durations between intervals are commonly prescribed using a fixed approach (e.g., 30 s between intervals). An alternative is the self-selected (SS) approach, in which trainees select their resting durations. Studies comparing the two approaches report mixed results. However, in these studies, trainees in the SS condition rested for as little or as long as they wished, leading to dissimilar total rest durations between conditions. Here, for the first time, we compare the two approaches while controlling for total rest duration.MethodsTwenty-four amateur adult male cyclists completed a familiarization session, followed by two counterbalanced cycling HIIT sessions. Each session was composed of nine, 30-s intervals, in which the goal was to accumulate as many watts as possible on an SRM ergometer. In the fixed condition, cyclists rested for 90 s between intervals. In the SS condition, cyclists had 720 s (i.e., 8  × 90 s) of rest to allocate in any way they wished. We measured and compared watts, heart rate, electromyography of the knee flexors and extensors, rating of perceived effort and fatigue, perception of autonomy and enjoyment. Additionally, a subsample of ten cyclists completed a retest of the SS condition.ResultsWith the exception of perception of autonomy, which was higher in the SS condition, outcomes were highly similar in both conditions. For example, the average aggregated differences were: 0.57 (95% CI − 8.94, 10.09) for watts; − 0.85 (95% CI − 2.89, 1.18) for heart rate; and 0.01 (95% CI − 0.29, 0.30) for rating of perceived effort (on a 0–10 scale). Additionally, the retest of the SS condition resulted in a similar rest allocation pattern across the intervals and in similar outcomes.ConclusionGiven the similarities in performance, physiological and psychological outcomes between the fixed and SS conditions, both can be equally utilized based on coaches’ and cyclists’ preferences and training goals.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40798-023-00601-8.