Enpp (ectonucleotide phosphodiesterase/pyrophosphatase) 6 is a membrane‐bound glycoprotein that hydrolyzes choline‐containing compounds such as lysophosphatidylcholine and glycerophosphorylcholine, and presumably participates in choline metabolism. The catalytic domain of mouse Enpp6 was expressed in HEK293T cells, purified using the TARGET tag/P20.1‐Sepharose system and crystallized. An X‐ray diffraction data set was collected to 1.8 Å resolution. The crystal belonged to space group P1, with unit‐cell parameters a = 63.7, b = 68.8, c = 69.7 Å, α = 60.6, β = 87.0, γ = 68.1°. Assuming the presence of two protein molecules per asymmetric unit, the solvent content was estimated to be 49.5%.