Mitochondrial disease (MD) generally refers to a group of disorders that are attributable to malfunctioning mitochondria that are unable to efficiently or effectively generate energy. Some of the most profound effects of MD are seen in the brain and the muscles, while other commonly affected organs include the heart, liver, nervous system, eyes, ears, and kidneys. One of the promising nutritional components, which may play a crucial role in the management of MD is omega-3 polyunsaturated fatty acids (n-3 PUFAs). Animal studies concluded that the omega-3 PUFAs, i.e., α-linolenic acid (ALA) and especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), have some positive effects on functional parameters of mitochondria in various mitochondrial dysfunction-related pathological conditions such as neurodegenerative diseases: Parkinson’s disease, Alzheimer’s disease, aging, cardiovascular diseases, diabetes, and reactive oxygen species (ROS)-induced damages. Supplementation with n-3 PUFAs from fish oil (FO) has shown mitochondrial neuroprotective effect in animal models of Parkinson’s disease and aging while clinical trials with patients have shown equivocal results. n-3 PUFAs protected cardiac mitochondria from Ca2+-induced swelling in isoproterenol-treated rats. In animal studies, DHA supplementation brought about significant changes in mitochondria membrane phospholipid components. A similar pattern was noted in cardiac mitochondria from a diabetic animal model.