During the American Civil War, Baker served as colonel of the 10th Minnesota Volunteer Infantry in the Union Army in 1862–1863.

[2] He was appointed Provost Marshal for the Department of Missouri, and served till the close of the war.

[2] In recognition of Baker's service, on January 13, 1866, President Andrew Johnson nominated Baker for appointment to the grade of brevet brigadier general to rank from March 13, 1865, and the U.S. Senate confirmed the appointment on March 12, 1866.

He then retired to a farm in Minnesota, and was appointed Commissioner of Pensions by President Grant from 1871 to 1875.

[1] Together with Judge Lorin Cray, Baker paid for the creation of a four-ton granite marker known as the "Hanging Monument", commemorating the mass execution of 38 Dakota men in Mankato on December 26, 1862.