Thomson was born in "Bhurtpore" (modern day Bharatpur, Rajasthan), India on April 1, 1832. He was educated in England and attended Addiscombe Military Seminary as a cadet. In 1853 he received a commission in the 53rd Bengal Native Infantry, a regiment in the British East India Company. During the Indian Mutiny of 1857, Thomson played a key role in the defense of Wheeler's Entrenchment during the Siege of Cawnpore. He was one of the few survivors of the siege and subsequent massacre at Sati Chaura Ghat .