We aimed to analyse cardiac autonomic control by assessing the post-exercise heart rate recovery (HRR) and physical fitness in children and adolescents with spina bifida (SB), compared to participants with typical development. A total of 124 participants, 42 with spina bifida (SB group) and 82 typical developmental controls (CO group) performed the arm cranking exercise test with a gas analysis system. HRR was determined at the first (HRR_1) and second (HRR_2) minute at recovery phase. Data are shown as [mean difference (95% CI)]. The SB group showed reduced HR reserve [14.5 (7.1–22.0) bmp, P<0.01], slower HRR_1 [12.4 (7.4–17.5) bpm, P<0.01] and HRR_2 [16.3 (10.6–21.9) bpm; P<0.01], lower VO2peak [VO2peak relative: 7.3 (4.2–10.3) mL·min−1·kg−1, P<0.01; VO2peak absolute: 0.42 (0.30–0.54) L·min−1, P<0.01], and lower O2 pulse [2.5 (1.8–3.2) mL·bpm, P<0.01] and ventilatory responses [13.5 (8.8–18.1) L·min−1, P<0.01] than the CO group. VE/VO2 was not different between groups [−2.82 (−5.77– −0.12); P=0.06], but the VE/VCO2 [−2.59 (−4.40–0.78); P<0.01] and the values of the anaerobic threshold corrected by body mass [−3.2 (−5.8– −0.6) mL·min−1·kg−1, P=0.01] were higher in the SB group than in the CO group. We concluded that children and adolescents with SB have reduced physical fitness and a slower HRR response after maximal effort.