In this study, the complete mitochondrial genome of Silurus cochinchinensis was reported to be 16,501 bp in length, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and one control region. The structural organization and gene order were equivalent to other bony fishes. The complete genome of S. cochinchinensis would provide the basic dataset for further research on phylogenetics and conservation genetics of catfishes.