Resting bradycardia is an important symptom for early diagnosis of anorexia nervosa (AN) during weight loss, and it improves with body-weight recovery. However, chronotropic incompetence (CI) in exercise is observed in some patients with AN despite amelioration of resting bradycardia in the recovery phase. We examined the relationship between CI in exercise and other parameters in patients with AN during the recovery phase. Ninety-two girls with AN (aged 13–20 years, median 15 years) performed cardiopulmonary exercise tolerance tests with a bicycle ergometer in the post-treatment recovery phase. Subjects with a peak-heart rate (HR) of < 160 beats/min (bpm) on subjective maximum loading were assigned to the CI+ group (n = 7), and those with a peak-HR of ≥ 160 bpm were assigned to the CI− group (n = 85). The peak-oxygen uptake (VO₂) of both groups was below the normal range. Although there was no difference in peak-VO₂ between these groups, both the resting-HR and ΔHR (peak-HR − resting-HR) were significantly lower in the CI+ group than in the CI− group (82 ± 8 vs. 93 ± 16 bpm, respectively; 72 ± 14 vs. 89 ± 13 bpm, respectively), suggesting lower exercise tolerance in patients with CI during the recovery phase of AN. Interestingly, the ΔVO₂/ΔHR value was higher in the CI+ group than in the CI− group (0.31 ± 0.13 vs. 0.26 ± 0.06, respectively), suggesting excessive stroke volume for maintaining the cardiac output in patients with CI during their recovery phase. These data suggest that CI could be an index of insufficient recovery of AN and utilized for ideal exercise treatments of patients with AN during the recovery phase.