Background and purpose The aim of this study was to investigate the influence of different physiotherapy protocols on heart rate variability (HRV) and hospital length of stay in older adults undergoing coronary artery bypass graft (CABG). Methods Randomized controlled trial with allocation and researcher blinding and intention‐to‐treat analysis. Forty‐eight patients undergoing CABG were randomly assigned to a control group (CG), early mobilization group (EMG), or virtual reality group (VRG). CG performed respiratory physiotherapy and metabolic exercises, the EMG performed cycle ergometer exercises and ambulation, and the VRG performed the same activities as the EMG, with the addition of two Nintendo Wii games during 3 postoperative days. The variables of heart rate variability on preoperative and fourth postoperative day, and time of discharge of hospital was analyzed. Results The VRG presented a shorter hospital length of stay (p = 0.03). The CG showed a decline in HRV from the preoperative period to fourth postoperative day on square root of the mean of the squared differences between successive RR intervals (33.18 ± 9.89–9.74 ± 6.88, p < 0.05), standard deviation of all RR intervals (25.48 ± 7.50–15.23 ± 11.27, p < 0.05), and dispersion of points perpendicular to identity line (28.26 ± 21.6–2.73 ± 1.31, p < 0.05). The EMG and VRG presented a higher cardiac autonomic modulation compared to the CG (p < 0.05), with improved parasympathetic activity. Conclusions Different protocols of physiotherapy intervention affected autonomic modulation of the heart rate and hospital length of stay in patients undergoing CABG.