Although it is considered to be a benign condition, previous studies have shown that a subset of patients with mitral valve prolapse (MVP) may be at risk of ventricular arrhythmia and sudden cardiac death (SCD). Previous studies have suggested that the interval between the peak and the end of the T wave (Tp-e) can be used as a marker for the transmural dispersion of repolarization. Increased Tp-e interval and Tp-e/QT ratio are associated with ventricular arrhythmias and SCD. The aim of this study was to assess alterations in ventricular repolarization by using the Tp-e interval and Tp-e/QT ratio in children with MVP and to investigate their relationships with the degree of valvular regurgitation. This study prospectively investigated 110 children with MVP and 107 age- and sex-matched healthy control subjects. Tp-e interval, Tp-e/QT ratio, and QT and QTc dispersions were measured from a 12-lead electrocardiogram and compared between groups. QT and QTc dispersions, Tp-e interval, and Tp-e/QTc ratio were found to be significantly higher in patients with MVP. A positive correlation was found between Tp-e/QTc ratio and increase in the degree of mitral regurgitation (MR) (p < 0.05; r = 0.2). However, the degree of MR was not associated with QT, QTc, or Tp-e intervals; QT, QTc, or Tp-e dispersions; or Tp-e/QT ratio (all p values > 0.05). Individuals with MVP may be more prone to ventricular arrhythmias due to prolonged QTd, QTcd, and Tp-e interval and increased Tp-e/QT and Tp-e/QTc ratios. Therefore, due to their longer life expectancy, children with MVP should be followed up on regarding life-threatening arrhythmias.