Chronic right ventricular (RV) apical pacing has been associated with deterioration of functional capacity and chronotropic incompetence during exercise testing in children. The effects of alternative pacing site on exercise performance in pediatric population remain unknown. We evaluated the influence of ventricular pacing site on exercise capacity in pediatric patients with complete congenital atrioventricular block requiring permanent pacemaker therapy. Sixty-four children paced from RV apex (n = 26), RV midseptum (n = 15) and left ventricular (LV) apex (n = 23) were studied cross-sectionally. Treadmill exercise stress testing was performed according to modified Bruce protocol. LV apical pacing was associated with greater exercise capacity. In comparison with the other study groups, children with RV apical pacing showed significantly lower VO₂peak (37 ± 4.11; p = 0.003), O₂ pulse (8.78 ± 1.15; p = 0.006), metabolic equivalents (7 ± 0.15; p = 0.001) and exercise time (6 ± 3.28; p = 0.03). Worse values in terms of maximum heart rate (139 ± 8.83 bpm; p = 0.008) and chronotropic index (0.6 ± 0.08; p = 0.002) were detected in the RV apical pacing group although maximal effort (respiratory exchange ratio) did not differ among groups (p = 0.216). Pacing from RV apex (odds ratio 9.4; confidence interval 2.5–18.32; Wald 4.91; p = 0.0036) and low peak heart rate achieved (odds ratio 3.66; confidence interval 0.19–7.4; Wald 4.083; p = 0.015) predicted significantly decrease in exercise capacity. Duration of pacing, gender, VVIR mode, baseline heart rate and QRS duration had not significant impact on exercise capacity. The site of ventricular pacing has the major impact on exercise capacity in children requiring permanent pacing. Among the sites assessed, LV apex is related to the better exercise performance.