In December 1910, Bertholf's tour aboard USRC " Bear" ended and he received orders assigning him to the command of , homeported in Detroit. Since "Morrill" was laid up for the winter, this gave him time to concentrate on his campaign to succeed Worth G. Ross as Captain-Commandant of the USRCS. Several senior captains were actively seeking the appointment and Bertholf was only 23rd on the seniority list. His dismissal from the Naval Academy was the lone black mark against him; however, his Congressional Gold Medal and service as commanding officer of "Bear" were all points in his favor. An endorsement by Walter Eli Clark, the district governor of Alaska, and Franklin MacVeagh, Secretary of the Treasury, finally helped him secure the nomination to the post. Bertholf was confirmed by the Senate on 15 June 1911 and became the fourth Captain-Commandant of the service. One of his first challenges was a reorganization of the RCS after the Treasury Secretary directed that operational control of the service's cutters be removed from the civilian Customs Collectors and assigned to the Revenue Cutter Service chain-of-command. This allowed Bertholf reorganize the RCS headquarters staff and to establish district offices in several cities on both coasts for better control of the cutters. In 1912, Bertholf was called to testify at the House Committee on Foreign Affairs hearings on implementation of the North Pacific Fur Seal Convention of 1911, a treaty designed to protect seals and otters from over hunting. His testimony dealt with the RCS role in enforcement of the treaty and how Bering Sea Patrol law enforcement would be made much easier by the inclusion of Russia and Japan and not just the United States and Great Britain.