Enterococcus faecalis is an important bacterium for use as a probiotic and is an opportunistic pathogen in human beings. The antibiotic resistance acquired by E. faecalis is restricted to antibiotics used in the clinical setting. While screening for alternative antibiotics for use against multidrug-resistant E. faecalis, we isolated a virulent enterococcal bacteriophage, SAP6, belonging to the family Siphoviridae. To our knowledge, this study is the first to report the complete genome sequence of bacteriophage SAP6, which might be used as a therapeutic agent in combination with alternative antibiotics for multidrug-resistant E. faecalis.