Streptococcus parauberis strain SK-417 was isolated from the brain of a diseased Sebastes ventricosus, collected from an aquaculture farm in April 2013 in Kagoshima Prefecture, Japan. The draft genome sequence, obtained with a 454 GS Junior sequencing system, consists of 33 large contigs of >500 bp, totaling 1,958,836 bp, and has a G+C content of 35.4%.