He was born 24 May 1774 in Dublin, descended of an ancient Catholic family from Co. Westmeath, the Magans of Umma-more (Emoe). His grandfather, James Magan, established a medical practice in Dublin, where he was succeeded by his eldest son, Richard. Thomas Magan, James's second son, became a woolen draper, establishing himself at 49 High St., Dublin. Active politically, Thomas represented Dundalk at the Catholic Convention of 1792. Loyal to the crown, however, he was named wool draper and mercer to the king in 1794, an honorary title he probably owed to his friend Francis Higgins, owner of a well-known government "print", The Freeman's Journal.
Magan was admitted to Trinity College, Dublin in 1788, although he did not attend before 1791. He joined the College Historical Society but was never active. In May 1794, he signed the oath of loyalty required of any aspiring Catholic barrister and went to London to study at Lincoln's Inn.
Returning to Dublin in 1796, he was admitted to the Irish Bar by King's Inns in Michelmas term. The published records of the King's Inns state he had been employed in the Irish revenue, but this is unconfirmed.
Magan's historical notoriety originates from a single act. During April–May 1798 he informed the government several times of the whereabouts of Lord Edward Fitzgerald on Thomas St., just as the latter prepared to take the field at the head of thousands of rebels. Lord Edward's apprehension on 19 May deprived the United Irishmen of their most charismatic leader. Magan was able to pass on this crucial intelligence to the Castle without being discovered, or even suspected during his lifetime, probably because of his otherwise unremarkable life. He had gained his intelligence through long involvement with the United Irishmen, eventually being elected to the committee responsible for Dublin. He hosted a meeting of this committee on the night of 17 May 1798. Lord Edward attended and may have passed the night in Magan's house. Magan duly passed this information on to the Dublin Castle the next day, provoking an unsuccessful attempt by Major Sirr to apprehend the rebel as he departed from the rear of 20 Usher's Island at dusk (the Watling St. affray).