Here, we report the whole-genome sequence of a methicillin-resistant Staphylococcus aureus strain harboring staphylococcal cassette chromosome mec (SCCmec) type IX, isolated from a fatal bacteremic pneumonia case. Genomic analysis revealed that the isolate was sequence type 9 and spa type t3446, carrying multiple antimicrobial resistance genes comprising mecA, blaZ, aac(6')-aph(2″), aadD, ant(6)-Ia, lsa(E), dfrG, tet(M), fexA, and lnu(B).