Individuals with Duchenne Muscular Dystrophy (DMD) have an impairment of cardiac autonomic function categorized by parasympathetic reduction and sympathetic predominance. The objective of this study was to assess the cardiac autonomic modulation of individuals with DMD undergoing therapy with Prednisone/Prednisolone and Deflazacort and compare with individuals with DMD without the use of these medications and a typically developed control group. Methods: A cross-sectional study was completed, wherein 40 boys were evaluated. The four treatment groups were: Deflazacort; Prednisone/Prednisolone; no corticoid use; and typical development. Heart Rate Variability (HRV) was investigated via linear indices (Time Domain and Frequency Domain) and non-linear indices Results: The results of this study revealed that individuals with DMD undertaking pharmacotherapies with Prednisolone demonstrated HRV comparable to the Control Typically Developed (CTD) group. In contrast, individuals with DMD undergoing pharmacotherapies with Deflazacort achieved lower HRV, akin to individuals with DMD without any medications, as demonstrated in the metrics: RMSSD; LF (n.u.), HF (n.u.), LF/HF; SD1, α1, and α1/α2, and a significant effect for SD1/SD2; %DET and Ratio; Shannon Entropy, 0 V%, 2 LV% and 2 ULV%. Conclusions: Corticosteroids have the potential to affect the cardiac autonomic modulation in adolescents with DMD. The use of Prednisone/Prednisolone appears to promote improved responses in terms of sympathovagal activity as opposed to Deflazacort.