Background: Obesity is a significant health problem with an increasing incidence, causing a low-grade systemic inflammatory state and being implicated in various chronic diseases. Moreover, obesity has been shown to cause mitochondrial dysfunction through oxidative stress and inflammation, eventually affecting energy metabolism. However, high-intensity interval training (HIIT) can improve mitochondrial efficiency through exercise-induced mitochondrial adaptations. This systematic review and meta-analysis aims to examine the potential effects of HIIT on mitochondrial-associated indices in obese and overweight adults. Methods: PubMed, Scopus, and Web of Science databases were searched. Results: Twenty-eight eligible studies were included, involving 530 participants. HIIT was found to significantly improve the activity of citrate synthase (CS), cytochrome C (COX-IV), beta-hydroxyacyl CoA-dehydrogenase (\beta-HAD), Complexes I-V as well as VO{}_2max in overweight and obese individuals, whereas no significant changes were shown in PGC-1\alpha and SIRT1. Interestingly, subgroup analyses revealed that CS, COX-IV, \beta-HAD, and Complexes I-V activity exhibited a significant improvement only in the healthy subgroup. Conclusions: Overall, HIIT can be utilized to enhance mitochondrial-associated indices in overweight and obese individuals. However, this improvement may be health status dependent.