Mitochondrial diseases (MDs) are a heterogeneous group of progressive multisystem disorders caused by impaired mitochondrial function. This study aimed to evaluate the clinical course and long-term development of 53 pediatric patients with MDs. Developmental function was evaluated at nine time points (two pre-diagnosis, one at diagnosis, and six post-diagnosis), with the developmental quotient (DQ) from the Korean infant and child development test (KICDT) assessing a child's developmental age (rather than chronological age). Additionally, disease-related clinical variables were reviewed, and clinical progress was determined through observation. Subgroup analyses by epilepsy severity, syndromic diagnosis, diffuse brain atrophy, and clinical rating were performed. The pre- and post-diagnosis results were compared by the paired t-test and Bonferroni correction. The pre-diagnostic, diagnostic, and post-diagnostic evaluations were compared using repeated measures ANOVA. Patients with diffuse brain atrophy at the first pre-diagnostic and second post-diagnostic evaluations showed lower DQs. Compared with patients with a mildly or severely deteriorating clinical course, those with an improving or static clinical course presented higher DQs at the pre-diagnostic and diagnostic evaluations. The age at onset of the first symptom correlated positively with the DQ post-diagnosis. Follow-up revealed consistent patterns of significant developmental deterioration during the lead time to diagnosis, with no significant decline post-diagnosis. The DQ is a feasible predictor and a measure of long-term functional development in children with MD. Early initiation of treatment may minimize developmental regression.