ABU DHABI—The U.S. is working to resolve a dispute with Turkey over its withdrawal from Syria, Secretary of State Mike Pompeo said Saturday, adding that it is continuing to negotiate the transfer of military responsibility and the fate of its Kurdish allies.

Turkish President Recep Tayyip Erdogan has rejected U.S. efforts to establish conditions for withdrawal from Syria, challenging the assertions of national security adviser John Bolton. He has rebuffed calls to protect Kurdish fighters Ankara characterizes as terrorists,...