Fitzgerald was born in Germantown, in Herkimer County, New York. His father was an Irish, and fought with the Continental Army, was wounded and received a pension. Thomas received a common school education and fought with the U.S. Army the War of 1812. He was severely wounded and afterwards taught school for a time in Marcellus, New York. In 1819 he moved to Boonville, Indiana, where he taught school and studied law. He was admitted to the bar in 1821 and began a practice in Booneville. He was a member of the State house of representatives in 1821 and from 1825 to 1827. He was a probate judge in Indiana in 1829.

In 1832, Fitzgerald was appointed keeper of the lighthouse at the mouth of the St. Joseph River and moved to St. Joseph, Michigan. He was clerk of Berrien County in 1834 and a regent of the University of Michigan in 1837. He was appointed bank commissioner in 1838 to investigate what were called "wildcat" banks and was served in the State house of representatives in 1839. He ran unsuccessfully for Lieutnant Governor in 1839 and was appointed as a Democrat to the U.S. Senate to fill the vacancy caused by the resignation of Lewis Cass, serving in the 30th Congress from June 8, 1848 until March 3, 1849. He moved to Niles, Michigan in 1851 and served as probate judge of Berrien County from 1852 to 1855. He died in Niles and is interred in Silverbrook Cemetery.