Age is an important determinant of heart rate variability (HRV) in healthy individuals. The incidence of arrhythmia is high in patients with mitral valve prolapse (MVP). However, the correlation of HRV in patients with MVP in different age groups is not well established. We presumed that increasing age would be prospectively associated with declining HRV measurement in MVP. Sixty patients with MVP and 120 control individuals were included and underwent 24 h HRV analysis. No significant difference was found in all parameters calculated in the time domain or in the frequency domain between the two groups. However, as patients’ age increased, a significant time domain (SDNN, RMSSD, NN50, and pNN50) decline was found in the MVP group, but not in the control group. This suggests that patients with MVP may have autonomic nervous system involvement that increases the risk of arrhythmia and heart disease with increasing age.