The aim of this systematic review with meta-analysis was to determine differences in cardiovascular autonomic parameters between patients with myasthenia gravis (MG) and healthy controls (HCs). Two reviewers searched four electronic databases, namely PubMed, Web of Science, EMBASE, and SCOPUS, from database inception to 7 July 2023 for studies investigating cardiovascular autonomic parameters in MG vs. HCs. A random-effects meta-analysis was performed to compute Hedges’ g ± 95% confidence intervals (CI). Out of a total of 2200 records, 8 observational studies with a sample size of 301 patients with MG and 454 HCs were included in the systematic review. Meta-analysis revealed lower values of expiration/inspiration ratio (g = −0.45, I2 = 74.7), baroreflex sensitivity (g = −0.56, 95%CI −0.80, −0.33; I2 = 0.3), percentage of adjacent NN intervals differing by more than 50 ms (g = −1.2, I2 = 82.8), square root of the mean of squared differences between successive beat intervals (g = −1.94, I2 = 95.1), mean of the standard deviations of all NN intervals (g = −0.83, 95%CI −1.37, −0.28; I2 = 55.5), and high frequency of HRV during tilt (g = −0.75, 95%CI −0.11, −0.39; I2 = 0). MG patients vs. HCs had higher systolic blood pressure (g = 0.39; I2 = 56.1), sympathovagal balance at rest/during tilt (LF/HF-RRIsupine, g = 0.44; I2 = 0; LF/HF-RRItilt, g = 0.86; I2 = 0; LF/HFtilt, g = 0.40; I2 = 0). As a group, MG patients have altered cardiac autonomic function, including decreased parasympathetic function, lower baroreflex sensitivity, and higher sympathovagal balance at rest and during orthostatic challenges.