Acer nikoense (Sapindaceae: Acer) is a deciduous tree, belonging to the Ser. Grisea of Sect. Trifoliata. Its complete genome sequence was obtained using genome Illumina pair-end sequencing data. It had a typical quadripartite structure with 155,952 bp in length, consisting of a large single-copy region (85,720 bp) and a small single-copy region (18,072 bp), as well as a pair of inverted repeats (26,080 bp). The total GC content was 37.9%. A total of 113 unique genes were annotated, including 30 tRNAs, 4 rRNAs, and 79 protein-coding genes. The phylogenetic analysis indicated that A. nikoense and A. triflorum were the most closely related.