His most noted service had been in connection with Alaska. In 1897 he, along with First Lieutenant David H. Jarvis and Dr. S. J. Call, made up the relief party which made the famous overland trip in mid-winter to Point Barrow, an epic journey that became known as the Alaska Overland Expedition. Congress voted him a gold medal for this relief of over two hundred American whalers in danger of starving when their vessels were trapped in the ice. In the winter of 1901, Bertholf made a trip across northern Siberia by sledge at the request of the Bureau of Education. The purpose of this mission was the purchase of a reindeer herd to be used by the Inuits of northern Alaska. He went on to command the famous cutter Bear on the Bering Sea Patrol.
He was appointed Captain-Commandant of the United States Revenue Cutter Service on 19 June 1911 and re-appointed to the same office in January 1915 when President Woodrow Wilson merged the Revenue Cutter Service with the Life-Saving Service to form the U.S. Coast Guard, a merger made possible through Bertholf's strong guidance and input. He served as one of the American delegates to the International Conference on Safety at Sea held in London in 1912 that led to the establishment of the International Ice Patrol. In addition to his duties as Captain Commandant of the Coast Guard, Bertholf also served as chairman of the Interdepartmental Board on International Ice Observation and Patrol in the North Atlantic and of the Board on Anchorage and Movements of Vessels.
During the First World War Captain Commandant Bertholf held the temporary rank of Commodore, the first officer of either the Revenue Cutter Service or Coast Guard to achieve flag rank. Upon his retirement as Commandant of the Coast Guard on 30 June 1919, he became one of the vice presidents of the American Bureau of Shipping and was "a most active, influential, and important factor" in the affairs of that institution. He also made quite an extensive European tour to expand this American organization in foreign fields. He died at his residence at Bretton Hall Hotel in New York City on 11 November 1921 and was buried with full military honors at Arlington National Cemetery.
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