A novel method for efficiently manufacturing a functional molecule with affinity for a target substance is provided along with a functional molecule manufactured by this method. The method for manufacturing a functional molecule includes binding, to a resin, a specific substance having a cleavable linker which is a site that is cleavable under a specific condition to prepare a specific-substance-bound resin, treating this specific-substance-bound resin with a solution comprising functional molecule candidates, and then cleaving the cleavable linker under the specific condition to select a functional molecule which has interacted specifically with the specific substance.