The complete mitogenome sequence of Spoon-billed sandpiper ( Eurynorhynchus pygmeus ) was reported in this study. The mitogenome was a circular molecule (16,709 bp) with a typical vertebrate mitogenome arrangement, which consisted of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding region (D-loop). The overall base composition was 31.3% A, 29.9% C, 13.8% G, and 25.0% T. The length of D-loop is 1155 bp in length, containing tandem repeats. Phylogenetic analyses based on the concatenated protein-coding genes indicated that the South Korean and Chinese E. pygmeus formed a group that was most closely related to Arenaria interpres .