Prior to the American Civil War, Humphreys was as a member of the Indiana House of Representatives (1849 to 1852, and January 8 to March 9, 1857), and an Indian agent for Utah.

At the end of the war, Humphreys resumed a career in politics, which included terms in Forty-fourth Congress (December 5, 1876 to March 3, 1877) and the Indiana Senate (1874 to 1876, 1878 to 1882, and 1896 to 1900).

Harrison H. Dodd, "grand commander" of the Sons of Liberty in Indiana, chose Humphreys as one of his major generals in a secret society who opposed the war.

[6] The military commission for the trial of Humphreys, Milligan, Horsey, and Bowles convened at Indianapolis on October 21, 1864, to consider five charges against the men: conspiracy against the U.S. government; offering aid and comfort to the Confederates; inciting insurrections; "disloyal practices"; and "violation of the laws of war.

"[7][8] The defendants were alleged to have established a secret organization that planned to liberate Confederates from Union prisoner-of-war camps in Illinois, Indiana, and Ohio; seize an arsenal to provide the freed prisoners with arms; raise an armed force to incite a general insurrection; join with the Confederates to invade Indiana, Illinois, and Kentucky; and make war on the U.S.

Scholars who studied the trials, which were highly publicized in the press, have proposed that they were prompted by partisan politics, convened before commission of biased military officers, failed to follow the rules of evidence, and used questionable informers as witnesses.

After Congress amended the Habeas Corpus Suspension Act of March 3, 1863, ending further suits in the civil courts from those who had been arbitrarily arrested during the war, Humphreys returned to a career in politics.

Although he lost his bid to win a seat in the Indiana General Assembly by a narrow margin in 1868,[16] Humphreys remained active in politics.

[16] Humphreys was elected as a Democrat to the Forty-fourth Congress to fill the vacancy caused by the resignation of James D. Williams and served from December 5, 1876, to March 3, 1877.