The NPC-associated SUMO protease Ulp1p regulates numerous cellular processes. The karyopherins bind the non-catalytic domain of Ulp1p and target Ulp1p to the NPC. Structures of the Kap121p–Ulp1p complex and the Kap60p–Ulp1p complex are reported. The non-catalytic domain of Ulp1p contains canonical NLSs. GTP-bound Gsp1p and Cse1p cooperate to release Ulp1p from the karyopherins.