This study reports the first isolation and characterization of a vanD5 genotype vancomycin-resistant Enterococcus faecium strain (E. faecium IPHb306) recovered from a 79-year-old Japanese female inpatient. Species identification was determined by biochemical testing, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and species-specific PCR. Susceptibility tests indicated that E. faecium IPHb306 was resistant to vancomycin but susceptible to teicoplanin. Southern hybridization analyses indicated that E. faecium IPHb306 harbored a vanD5 gene cluster on chromosomal DNA. Growth curve analyses showed that a vancomycin resistance phenotype could be inducible. Sequencing analyses of the vanD5 gene cluster and the ddl gene demonstrated several point mutations were present. Because this strain belongs to ST203, a major hospital-adapted lineage, spread of the vanD5 genotype E. faecium ST203 is considered a clinical threat in Japan.