We report here the draft genome sequence of Leifsonia sp. strain NCR5, a Gram-positive actinomycete isolated from Carpobrotus rossii (Haw.) Schwantes rhizosphere. The de novo genome of Leifsonia sp. strain NCR5 was assembled with 69 scaffolds and a G+C content of 69%, was 4.2 Mb in length, and contained 3,952 coding sequences.