Purpose: This study aimed to investigate the effectiveness of different physical therapy protocols on the autonomic modulation of heart rate, time of invasive mechanical ventilation (IMV), and length of hospital stay. Methods: This was a randomized clinical study with 20 children on IMV in an intensive care unit (ICU), between July 2018 and September 2019. The control group (n = 10) performed the hospital's physical therapy protocol and the experimental group (n = 10) performed the physical therapy protocol based on physical exercise. Results: Higher values of heart rate variability were found in the experimental group, both in individual and intergroup analyses. There was a significant reduction in the time of IMV and ICU stay. Conclusion: There was an improvement in heart rate variability, reduced time on mechanical ventilation and length of stay in the ICU in individuals who performed the study protocol.