Provided is a novel method for producing a Wnt protein, which method comprises(1) a step of performing affinity purification targeting afamin to obtain a Wnt protein from a culture product, and/or(2) a step of performing affinity purification to obtain a Wnt protein in the form of a complex with afamin from a culture product.The method enables a Wnt protein having high Wnt activity to be produced in a simple and brief manner without use of special equipment.