Fagus multinervis is an endemic plant found in Ulleungdo Island in Korea. We present a second complete chloroplast genome of Fagus multinervis. The length of chloroplast genome is 158,349 bp, consisting of four subregions: 87,660 bp of LSC and 18,903 bp of SSC regions separated by a pair of 25,893 bp of IR regions. It includes 128 genes (83 protein-coding genes, eight rRNAs, and 37 tRNAs). There are two SNPs and two INDELs between two accessions of F. multinervis. The phylogenetic tree shows that the two accessions of F. multinervis form a clade, sister to F. engleriana.