He served as Brevet Brigadier General in the Union army during the American Civil War but was removed from command by John Gibbon for failure to suppress a mutiny by the 34th New York Infantry Regiment.

He was cleared by a court of inquiry of any wrongdoing and sent to command the District of Iowa (including the Territory of North Dakota) in the Department of the Northwest during the Sioux Wars.

[8] At the outbreak of the Civil War, Sully commanded US troops that occupied the city of St. Joseph, Missouri, due to secessionist uprisings[12] through November 1861.

[3] He returned East and helped build defenses around Washington, D.C.[13] Sully was promoted to colonel of the 1st Minnesota Infantry Regiment on March 4, 1862.

[17] Sully did not meet up with Sibley due to delays in troop movements caused by low water levels of the Missouri river.

[19] On September 3, 1863, at the Battle of Whitestone Hill,[20] Sully's troops demolished a village of approximately 500 tipis of Blackfeet, Dakota, Hunkpapa, Lakota, and Yankton.

[21] A scouting party from the 6th Iowa Cavalry Regiment, located the native American village and requested reinforcements from Sully.

[23] Modern historians estimate between 150[19] to 200 plus[24] native Americans killed with 156 prisoners taken[19] and U.S. troops suffering 22 dead and 38 wounded.

[26][27] In July 1864, Sully led the 30th Wisconsin Infantry Regiment to build Fort Rice as a base of operations for expeditions against the Sioux.

[29] Sully organized his troops into a hollow square and advanced on the village, allowing his artillery to dominate and avoiding hand-to-hand combat.

[32] The U.S. troops destroyed the village with artillery, took possession of the hilltop,[33] and drove the remaining Sioux into the badlands near the present-day Theodore Roosevelt National Park.

[2] With the end of the Civil War, Sully's commission as a brigadier general expired and he reverted to the rank of major in the regular army.

[13] From February to September 1867, he served as a member of the Interior Department and visited multiple Sioux tribes along the Platte and Upper Missouri Rivers.

[36] In 1867, he was scrutinized for his harsh treatment of native Americans by the committee on Indian Affairs led by James R. Doolittle.

[21] In September 1868, Sully led 500 men out of Fort Dodge and into Indian territory to punish "hostiles" responsible for raids into Kansas.

General Philip Sheridan arrived and resolved the dispute by selecting Custer to lead the expedition and sending Sully to Fort Harker.

[4] The couple had a son together, however, soon after childbirth, Manuela died in 1852, possibly from eating poisoned fruit from a rejected suitor, or from cholera.

[39] In 1866, Sully married Sophia Webster,[40] a resident of Richmond, Virginia, and Confederate sympathizer during the Civil War.

[45] Several of Sully's sketches of the Siege of Veracruz and his description of the battle from a letter were published in a 1914 article in The New York Times.