Returning to Iowa, Stanton was elected as a Republican to the State House of Representatives for the period 1862–1864.

Stanton did not stay long in the infantry, becoming an Additional Paymaster in the Volunteer Army in October the same year.

He received a brevet promotion for gallantry at the Battle of Powder River, and later commanded the citizens who joined Crook, but did not thereafter serve at the frontier.

[4][5] In 1895, Stanton was appointed Paymaster-General of the United States Army, succeeding William Smith.

[6][7] Thaddeus Harlan Stanton died in Omaha on January 23, 1900, and was buried in Arlington National Cemetery.