Thomson offered the Irishwoman basic medicine in the form of castor oil which improved her health. This made Thomson realize how medicine could be an asset in his work. This prompted him to change his plans of going abroad as a religious missionary and instead pursue medicine as his course of theology. After he completed his medical training, Thomson joined the Edinburgh Medical Missionary Society (EMMS). Thomson was first introduced to the Edinburgh Medical Missionary Society in 1854 through an essay competition. Thomson submitted an essay that didn't end up winning but was highly praised by one of the judges, Rev. Dr. Guthrie. Guthrie and other members of the society pushed Thomson to publish his essay which he did. In this essay, Thomson detailed the role the Church should play in the lives of the poor at the time. Following this first encounter with EMMS, Dr. Thomson was asked to take a superintendent position at the 39 Cowgate dispensary. This dispensary was first established by Dr. Peter David Handyside and it was Dr. Handyside and a colleague that convinced Dr. Thomson to take over that dispensary. During his time as the superintendent of the dispensary, Dr. Thomson created a training institution out of the dispensary. The Medical Missionary Society at the time gave an annual grant so that their current medical students would have access to the dispensary. These students were unreliable which prompted Dr. Thomson to urge the Society for more money to fund a training school. After securing funds from a friend, Dr. Thomson set up the Medical Mission Dispensary and Training Institution. Through this, he and his successors, John Lowe and Sargood Fry, were able to train at least 200 medical missionaries for the Protestant Church. In 1870, after working at 39 Cowgate and with EMMS for 11 years, Dr. Thomson felt that he needed to step away from the society. In an article published after Dr. Thomson's death, the editor of "Medical Missions at Home and Abroad", writes his theory on why Dr. Thomson resigned. According to the editor, a dispute between Thomson and the directors of EMMS over whether or not a student was qualified to be a medical missionary led to Dr. Thomson losing the respect of his students and his authority as their instructor. This then prompted his resignation and departure from the Society. A year after leaving 39 Cowgate and the Edinburgh Medical Missionary Society, Dr. Thomson wrote that throughout the months he was away from the dispensary he was able to connect more with god. In addition to reconnecting with his religious beliefs, Dr. Thomson began missionary work in The Canongate and set up a hospital there.