Sesame (Sesamum indicum L.), an important oilseed crop, has garnered considerable interest. The nuclear and chloroplast genomes of sesame have been extensively applied to sesame genetics and genomics research. The mitochondrial (mt) genome of sesame, however, has not been sequenced and annotated. In order to solve this issue, we reconstructed the first mt genome of sesame using third-generation sequencing data. The sesame mt genome was 724,998 bp in size and had 22 circular chromosomes. A total of 66 genes were annotated, including 37 protein-coding genes, 26 transfer RNAs, and three ribosomal RNAs. We investigated the codon usage patterns, simple sequence repeats, long tandem repeats, and dispersed repeats of the sesame mt genome. Furthermore, we investigated the DNA transfer from chloroplast to mitochondrion and compared the sesame mt genome to two other Lamiales mt genomes. Given the economic importance of this crop, our presented sesame mt genome is a valuable genomic resource and will allow for more comprehensive studies on sesame and related species.