To determine whether prior type 2 diabetes (T2D) treatment or glycemic control over time are independently associated with heart rate variability (HRV) and whether the presence of cardiac autonomic dysfunction is associated with arterial stiffness in young adults with youth-onset T2D enrolled in the Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY) study. Heartbeats over 10 min were measured to derive the normal R-Rs (NN intervals). Outcomes included the standard deviation of the NN intervals (SDNN), the root mean square differences of successive NN intervals (RMSSD), percent of NN beats that differ by more than 50 ms (PNN50), and the low-frequency (LF) power domain, high-frequency (HF) power domain, and their ratio (LF:HF). Autonomic dysfunction was defined as ≥3 of 5 abnormal HRV indices compared with obese controls from a separate study. A total of 397 TODAY participants were evaluated 7 years after randomization. TODAY participants had reduced HRV (SDNN; 57.9 ± 29.6 ms vs. controls 67.1 ± 25.4 ms; < 0.0001) with parasympathetic loss (RMSSD; 53.0 ± 36.6 ms vs. controls 67.9 ± 35.2 ms; < 0.0001) with sympathetic overdrive (LF:HF ratio; 1.4 ± 1.7 vs. controls 1.0 ± 1.1; < 0.0001). Cardiac autonomic dysfunction was present in 8% of TODAY participants, and these participants had greater pulse wave velocity compared with those without dysfunction ( = 0.0001). HRV did not differ by randomized treatment, but higher hemoglobin A1c (HbA ) over time was independently associated with lower SDNN and RMSSD and higher LF:HF ratio after adjustment for age, race-ethnicity, sex, and body mass index. Young adults with youth-onset T2D show evidence of cardiac autonomic dysfunction with both parasympathetic and sympathetic impairments that are associated with higher HbA .