He was the son of James and Elizabeth (née Lawler) Fitzpatrick and born in the Headfort Arms Hotel, Virginia where his parents were the proprietors.

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.

During this time Thomas Fitzpatrick also practiced as a doctor in the County 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.

[1] On his return to England, 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.