March 4, 1897, President McKinley made him secretary of war. He held the position for over two years, through the period of the war with Spain.
He was appointed United States senator September 27, 1902, to fill the vacancy made by the death of Senator McMillan; and in 1903 he was elected senator from Michigan for the term expiring 1907.
In 1861 he married Annette Henry, of Grand Rapids, Michigan. They have had nine children, five of whom are living. Senator Alger is considerate and kindly in all the relations of life. His charities extend in many directions, but boys, and especially newsboys are the particular object of his interest. It was the newsboys of Detroit who started the call: "What's the matter with Alger He's all right!" which was first heard at the Chicago convention of 1888. It went as a catchword all over the country, for all parties, and among all classes; but it was first applied to General Alger at Detroit.