Thomas was born on 3 August 1823, in Waterford. His parents were Thomas and Alicia (nee Quan). He was educated at Clongowes Wood College and Stoneyhurst College, the traditional English public school for young Catholic gentlemen. He returned to Dublin in 1843 and studied for the Bar. There he met writers of  'The Nation'. Meagher and his father attended one of O'Connell's 'monster' meetings in Lismore in September 1843. He became an ardent supporter of the Repeal movement and a founder of the Irish Confederation. Meagher spoke at many meetings. In 1848 he was arrested after the abortive rising lead by William Smith O'Brien. He was sentenced to death but this was commuted to penal servitude for life in Van Diemen's Land. He escaped to America in 1852.

Meagher became a member of the New York bar, a journalist, a publisher and one of the best known lecturers in the country. He helped John Mitchell to found 'The Citizen' newspaper. However with the outbreak of Civil War both ended up on different sides. Mitchell fought with the Southern states while Meagher not only supported the North but also founded the Irish Brigade, and fought with them as their Brigadier General. After the war he became acting governor of Montana territory. He is credited with having introduced the Tricolour as the National flag of Ireland. It is thought to have been flown for the first time from the former Wolfe Tone Meeting House on The Mall, in Waterford in March 1848. On 1 July 1867 he disappeared overboard in what is believed to have been an accident, while travelling on the Missouri.