Thomas Flintoff was educated privately and qualified as a member of the Royal College of Veterinary Surgeons (MRCVS) at the New Edinburgh Veterinary College in April 1875. In June that year entered the Royal Artillery as an officer in the Army Veterinary Department. In 1878 he transferred to the 8th Hussars and served with that regiment in the Afghan War (1879-1880). In 1885 he married Kate Hannah Frost, with whom he had one son. In June 1891 he was transferred to the 2nd Lifeguards regiment, and promoted to veterinary major in June 1895. He arrived in South Africa in October 1899 to serve in the Anglo-boer War (1899-1902) and was promoted to lieutenant-colonel in 1901. His war service was further recognised by the award of the Queen's Medal and by his being created a companion of the Distinguished Service Order (DSO) in June 1902.
After the war, in August 1903, he assumed duty as the first chief veterinary surgeon of the Orange River Colony with two veterinary surgeons in his department, A.G. Grist* and D.A.D. Aitchison. In May 1904 he represented the Orange River Colony at the Inter-Colonial Veterinary Conference in Cape Town (which dealt mainly with East Coast Fever), and in August that year left for England where he attended a four month course at the Royal Veterinary College, London. He resigned his post in July 1905 and returned to England. He was succeeded by Grist.