Allee filled the vacancy in the term commencing March 4, 1901. During this term, he served with the Republican majority in the 58th and 59th Congress. In the 58th Congress he was Chairman of the Committee on Indian Depredations until December 14, 1904, when he left the committee to become chairman of the Committee on the Organization, Conduct, and Expenditures of the Executive Departments. During the 59th Congress, he chaired the Committee on Railroads. In all, he served from March 2, 1903 until March 4, 1907, during the administration of U.S. President Theodore Roosevelt.