This study: 1) compared the physiological responses and performance during a high-intensity interval training (HIIT) session incorporating externally-regulated (ER) and self-selected (SS) recovery periods; and 2) examined the psychophysiological cues underpinning self-selected recovery durations. Following an incremental maximal exercise test to determine maximal aerobic speed (MAS), fourteen recreationally-active males completed two HIIT sessions on a non-motorised treadmill. Participants performed 12 x 30s running intervals at a target intensity of 105% MAS interspersed with 30s (ER) or SS recovery periods. During SS, participants were instructed to provide themselves with sufficient recovery to complete all 12 efforts at the required intensity. A semi-structured interview was undertaken following the completion of SS. Mean recovery duration was longer during SS (51 ± 15s) compared to ER (30 ± 0s; P<0.001; d=1.46 ± 0.46). Between-interval heart rate recovery was higher (SS: 19 ± 9 b·min-1; ER: 8 ± 5 b·min-1; P<0.001; d=1.43 ± 0.43) and absolute time ≥90% maximal heart rate (HRmax) was lower (SS: 335 ± 193s; ER: 433 ± 147s; P=0.075; d=0.52 ± 0.39) during SS compared to ER. Relative time ≥105% MAS was greater during SS (90 ± 6%) compared to ER (74 ± 20%; P<0.01; d=0.87 ± 0.40). Different sources of afferent information underpinned decision-making during SS. The extended durations of recovery during SS resulted in a reduced time ≥90% HRmax but enhanced time ≥105% MAS, compared with ER exercise. Differences in the afferent cue utilization of participants likely explain the large levels of inter-individual variability observed.