The present study was conceived with the objective to measure Heart Rate Variability in children with Attention–deficit/hyperactivity disorder (ADHD) before and after treatment with Methylphenidate. ADHD is associated with autonomic dysfunction which gets further modulated with drug therapy. There are few prospective studies to evaluate the changes of HRV parameters before and after methylphenidate treatment in drug naive patients with ADHD. Baseline ADHD Conners rating score, Vanderbilt ADHD score, Clinical Global Impression score and HRV was recorded. The patients then received methylphenidate medication for a period of 12 weeks. The above parameters were repeated at 12 weeks of study period. There was a significant improvement (decrease) in the Conners scores, Vanderbilt ADHD score and Clinical Global Impression score . HRV parameters showed a significant increase in the Low Frequency in normalized units (LF nu) a significant decrease in absolute power and normalized units of High Frequency in (HF) after methylphenidate treatment.  The increase in LF indicates an enhanced sympathetic activity whereas the decrease in HF indicates a decrease in the Parasympathetic activity.  The LF: HF ratio a marker of sympathovagal balance showed a significant increase after 12 weeks of MPH treatment. On the Time Domain Parameters the RMSSD decreased significantly after methylphenidate treatment. The present study shows that with methylphenidate therapy as the ADHD scores improved the autonomic balance shifted in favour of sympathetic preponderance. Moreover reduction in RMSSD warrants cautious use of methylphenidate in patients vulnerable to cardiac arrhythmias.