From a privileged upbringing Thomas was educated at St. Patrick's, Carlow College, a school well noted for turning out many fine Catholic theologians. However his university education at Trinity College, Dublin enabled him to distinguish himself in medicine where he qualified with a BA in 1853, MA in 1854, MB and MD by 1856.
Thomas Fitzpatrick practiced as a doctor in the Co. Cavan village of Mullagh before entering service during 1856 with the British East India Company as an assistant surgeon, an experience which was to leave a lasting impression on him, through his future attitudes towards primitive medicine, magic and religion.
Thomas Fitzpatrick took up a position with St. Bartholomew's Hospital in London and in 1868 he became a member of the Royal College of Physicians. He took up a private practice near Hyde Park, London.
He was married to Agnes Letitia (née Robinson) in May 1865.