Through his father's family, he was a first cousin of Eleazar A. Paine, who would also serve as a general in the Union Army in the Civil War.

[2] With the outbreak of the Civil War, Paine entered the Union army as the colonel of the 4th Wisconsin Infantry Regiment.

On April 9, 1863, President Abraham Lincoln appointed Paine brigadier general of volunteers, to rank from March 13, 1863.

These included involvement in the Vicksburg campaign, the capture of New Orleans, the Battle of Baton Rouge, and the Bayou Teche offensive.

[4] With the Third Division of the Army of the Gulf, he took part in an assault on Priest Gap during the siege and Battle of Port Hudson in Louisiana.

[3] On December 11, 1866, President Andrew Johnson nominated Paine for appointment to the brevet grade of major general of volunteers, to rank from March 13, 1865.

He was a delegate to the 1866 National Union Convention in Philadelphia, which was attempting to encourage support for President Andrew Johnson in advance of the mid-term elections.

In 1879, he was appointed by President Rutherford B. Hayes as the United States Commissioner of Patents, serving in that post for two years.