Abstract: Individuals with comorbid rapid eye movement (REM) sleep behaviour disorder (RBD) and neurotrauma (NT; defined by traumatic brain injury and post‐traumatic stress disorder) have an earlier age of RBD symptom onset, increased RBD‐related symptom severity and more neurological features indicative of prodromal synucleinopathy compared to RBD only. An early sign of neurodegenerative condition is autonomic dysfunction, which we sought to evaluate by examining heart rate variability during sleep. Participants with overnight polysomnography were recruited from the Veterans Affairs Portland Health Care System. Veterans without NT or RBD (controls, n = 19), with RBD only (RBD, n = 14), and with RBD and NT (RBD+NT, n = 19) were evaluated. Eligible 5‐min non‐REM (NREM) and REM epochs without apneas/hypopneas, microarousals, and ectopic beats were analysed for frequency and time domain (e.g., low‐frequency [LF] power; high‐frequency [HF] power; root mean square of successive R–R intervals [RMSSD]; percentage of R–R intervals that vary ≥50 ms [pNN50]) heart rate variability outcomes. Heart rate did not significantly differ between groups in any sleep stage. Time domain and frequency domain variables (e.g., LF power, HF power, RMSSD, and pNN50) were significantly reduced in the RBD+NT group compared to the controls and RBD‐only group during NREM sleep. There were no group differences detected during REM sleep. These data suggest significant reductions in heart rate variability during NREM sleep in RBD+NT participants, suggesting greater autonomic dysfunction compared to controls or RBD alone. Heart rate variability during sleep may be an early, promising biomarker, yielding mechanistic insight for diagnosis and prognosis of early neurodegeneration in this vulnerable population.