Background Inflammation caused by chronic lung disease in childhood may lead to delayed heart rate recovery (HRR) however, there is lack of evidence on HRR in this population. The aim was to assess HRR after functional capacity testing in asthmatic children and adolescents and to compare with severity and disease control. Method This was a study secondary to a randomized control trial. The modified shuttle test (MST) was performed to assess functional capacity and HRR. This is an externally cadenced test in which the distance walked is the outcome. HRR was assessed after MST and was defined as HR at exercise peak minus HR in the second minute after the end of exercise. Asthma control was assessed by the Asthma Control Test (ACT). Data normality was tested by Shapiro Wilk and the comparison between groups was made by Student’s t test or Mann Whitney test for numerical variables, and by Chi-square test for categorical variables. Statistical significance was considered when p < 0.05. SPSS version 20 was used in the analyzes. Results The sample included 77 patients diagnosed with asthma (asthma group - AG) who were regularly treated for asthma. Control group (CG) consisted of 44 volunteers considered healthy, matched in age and gender to AG. The median age of CG was 12 (10–14) years and in AG 11 (9–13 years) being classified as mild to moderate asthmatic, and 57% of the sample had controlled asthma by ACT. Distance walked in the CG was 952 ± 286 m and AG 799 ± 313 m, p = 0.001. HRR was more efficient in CG (79 ± 15 bpm) compared to AG (69 ± 12 bpm), p = 0.001. The mild (69 ± 12 beats) and severe (72 ± 15 beats) AG presented worse HRR compared to control group (79 ± 15 bpm), p < 0.05. Conclusions Asthmatic children and adolescents have delayed HRR after modified Shuttle test compared to their peers, suggesting that asthma leads to autonomic nervous system imbalance. Trial registration: Registered in Clinical Trials under number NCT02383069 and approved by the Universidade Nove de Julho - UNINOVE Research Ethics Committee, protocol number 738192/2014.