This is the first document concerning human case of bacteremia due to Streptococcus suis serotype 5 in Japan. We confirmed the novel sequence type 752 of this isolate. Both sly (encoding the hemolysin suilysin) and mrp (encoding a muramidase-released protein) were detected with no amplification of epf (encoding the extracellular factor), showing the virulence-associated gene profiling. This isolate had both tet(O) and erm(B) as the antimicrobial resistance genes.