Nicholls joined the Confederate Army in 1861 as a captain in the 8th Louisiana Infantry Regiment and participated in the First Battle of Bull Run and in the Shenandoah Valley Campaign in Virginia, where he lost his left arm. In July 1862 he became colonel of the just formed 15th Louisiana Infantry. On October 14, 1862, Nicholls was promoted to the rank of brigadier general and given command of a brigade of Louisiana infantry. During the Battle of Chancellorsville, Virginia, in May 1863, a shell ripped off Nicholls' left foot. According to James Whitcomb Brougher, Sr., in Life and Laughter, he lost an eye at Richmond. Disabled and unfit for further field command, he was transferred to the Trans-Mississippi Department to direct the Volunteer and Conscript Bureau until the end of the war.
Postbellum
After the war, Nicholls returned to his law practice. In 1876, he ran for governor against the Republican Stephen B. Packard. The outcome was disputed, and both men claimed victory. Nicholls garnered a majority of 8,000 votes, but the Republican-controlled State Returning Board cited irregularities and declared Packard the winner. As part of the Compromise of 1877 to resolve the disputed presidential election of 1876, President Hayes recognized the Democrat Nicholls as the winner. During his first term, he battled political corruption, which was epitomized by Samuel James, the operator of the convict lease system, state Treasurer Edward A. Burke, and Lieutenant Governor Louis A. Wiltz, who supported the corrupt Louisiana Lottery. Nicholls chaired the Louisiana Constitutional Convention of 1879, and returned the state capital from New Orleans to Baton Rouge. Nicholls was governor of Louisiana in 1891, the year eleven Italians were lynched in New Orleans. Shortly before the incident, as thousands of angry protesters gathered near the Parish Prison, the Italian consul in New Orleans sought the governor's help. Nicholls declined to intervene. After his tenure as governor closed, Nicholls became Chief Justice of the Louisiana Supreme Court in 1892, a post which he held until 1911. He also grew sugarcane and other crops on his Ridgefield Plantation near Thibodaux, the seat of Lafourche Parish. He died at Ridgefield. Francis and Caroline Nicholls, Thomas Clark Nicholls, and other family members are interred in St. John's Episcopal Church and Cemetery in Thibodaux.
Memorialization
From 1913 to about 1950, there was a vocational school at 3649 Laurel Street in New Orleans named for Nicholls. It opened as the Francis T. Nicholls Industrial School for Girls, and offered secondary vocational training, concentrating on apparel manufacturing. The school was later renamed Nicholls Vocational School for Girls, and even later Nicholls Evening Vocational School. In 1940, a new public high school, Francis T. Nicholls High School, was opened at 3820 St. Claude Avenue in New Orleans. In the late 1990s the high school was renamed for former slave and abolitionist leader Frederick Douglass. It is now a charter school, part of the KIPP Family Schools and known as KIPP Renaissance High School. During the 1960s, the school was integrated and black students fought to change the team names from The Rebels and the mascot from the Confederate flag to the current Bobcat. There is a "Governor Nicholls Street" in New Orleans. Where it meets the Mississippi River near the downriver end of the French Quarter, there is a Governor Nicholls Street Wharf. Atop the wharf shed there, the United States Coast Guard built a manned control tower with a red and green traffic signal to control vessel traffic rounding Algiers Point. When speaking to the controller via marine VHF radio, mariners address him or her familiarly as "Governor Nick." In Baton Rouge, there is a sculpture of Nicholls by Isidore Konti. Nicholls State University, founded in 1948, is a public university located in Thibodaux, Louisiana. Nicholls is part of the University of Louisiana System. Originally called Francis T. Nicholls Junior College, the university is named for Francis T. Nicholls. He is played by James Bearden in the 1999 HBO original film Vendetta.