Medicago archiducis-nicolai Sirj. is a well-known high-quality forage as its good palatability and strong tolerance to drought, cold and saline-alkali stress. Here, the complete chloroplast genome sequence of M. archiducis-nicolai was reported. The size of the complete chloroplast genome is 127,072 bp in length. The chloroplast genome has no inverted repeat (IR) regions, which is very common in the family Fabaceae. The M. archiducis-nicolai chloroplast genome encodes 106 genes: 72 protein-coding genes, 30 tRNAs, and 4 rRNAs. The phylogenetic analysis result strongly suggested that M. archiducis-nicolai is a distinct lineage in Medicago, being sister to highly supported clade composed of three species (M. hybrida, M. papillosa and M. sativa).