Logan graduated in law from the University of Louisville (Kentucky) in 1851. He served as a Democratic congressman (1859–61) from Illinois, resigning his seat to join the Union Army as colonel of the 31st Illinois Infantry, which he had organized. He served under General Ulysses S. Grant until the capture of Vicksburg (July 1863), rising to the rank of major general of volunteers. In 1864 Logan succeeded General James McPherson as commander of the Army of the Tennessee but was later relieved of his command, apparently because General William T. Sherman felt Logan did not pay enough attention to logistics.

After the war, Logan, by then a Republican, represented Illinois in the U.S. House of Representatives (1867–71) and the Senate (1871–77, 1879–86). He helped found (1865) the Grand Army of the Republic (GAR), an organization of Union Army veterans, and was its head for three successive terms. In 1868, as commander in chief of the GAR, he inaugurated the observance of Memorial, or Decoration, Day when he asked GAR members to decorate soldiers' graves with flowers on May 30.