While Coenzyme Q₁₀ (CoQ₁₀) is thought to be effective for the treatment of a variety of diseases, it limits its cellular uptake. Because of the hydrophobic nature of CoQ₁₀, it is reasonable to assume that it could be encapsulated within a liposomal carrier. Several reports regarding the packaging of CoQ₁₀ in liposomes have appeared, but detailed investigations of the preparation of CoQ₁₀ encapsulated liposomes have not been reported. As a result, information regarding the optimal method of packaging CoQ₁₀ in liposomes is not available. In this study, several types of liposomes were prepared using different methods and their characteristics were compared. Since CoQ₁₀ is mainly located in the inner mitochondrial membrane, a liposome that targets mitochondria, a MITO-Porter, was used as a model liposome. It was possible to incorporate high levels of CoQ₁₀ into the carrier. Transmission electron microscopy analyses showed that an empty MITO-Porter and the CoQ₁₀-MITO-Porter were structurally different from one another. Even though significant structural differences were observed, mitochondrial delivery was not affected in mitochondrial disease fibroblast cells, as evidenced by confocal laser scanning microscopy observations. The results reported herein suggest that the CoQ₁₀-MITO-Porter might be a suitable candidate for the potential medical therapy of mitochondria-related diseases.