William was educated at Glasgow University, qualifying LR.C.P., L.R.C.S. as well as M.B. in 1880.
On 30th July 1881 he took up a commission at the rank of Surgeon Captain in the Medical Services, then gained promotion to Major on 30th May 1893. In 1897 he was appointed Principal Medical Officer for the International occupation of Crete during the troubles there, and for his service was appointed a Commander of the Order of St Michael and St George in 1899. He next saw active service in the South African War, from 1899 to 1900, whilst on the Staff of the Natal Army. He was present at the Relief of Ladysmih, and operations in Natal and Eastern Transvaal, being awarded the Victoria Cross �At Colenso, on December 15th 1899, the wounded of the 14th and 66th Batteries, Royal Field Artillery, were lying in an advanced donga close in the rear of the guns without any medical officer to attend to them, and when a message was sent back asking for assistance, Major W. Babtie, R A.M.C., rode up under a heavy rifle fire, his pony being hit three times. When he arrived at the donga, where the wounded were lying in sheltered corners, he attended to them all, going from place to place exposed to the heavy rifle fire which greeted anyone who showed himself. Later on in the day, Major Babtie went out with Captain Congreve to bring in Lieutenant Roberts, who was lying wounded on the veldt. This also was under a heavy fire.� [L.G. 20/4/1900]. Additionally, for his service in this war he was mentioned in despatched, received the Queen�s South African Medal with 5 clasps, and gained special promotion to the rank of Lieutenant Colonel on 29th November 1900. From 1901 to 1906, he took up the appointment of Assistant Director-General A.M.S. in charge of personnel at the War Office, and in 1901 was appointed Knight of Grace of St John of Jerusalem. On 12th March 1907 he was promoted to the rank of Colonel, and served as Inspector of medical services from 12th March 1907 to 5th March 1910.
He then took up the appointment of Deputy Director-General, with a temporary rank of surgeon General. In 1912 he was appointed Companion of the Order of the Bath (Military), and in 1914 was appointed King�s Honorary Surgeon.
On 22nd March 1914 he went to India to fill the appointment of Director Medical Services there, taking over from Sir Arthur Thomas Sloggett. On 5th June 1915 he left India to take up a newly formed position of Principal Director Medical Services, Mediterranean, beginning from 15th June 1915. This new position had been appointed by the Army Council due to a demand for co-ordination of medical administration in Egypt, the Dardanelles, Malta, Gibraltar and Macedonia. After a month he was able to set up an office for himself and his staff in Alexander, which moved to Cairo by the end of the year. His role as P.D.M.S. was to inspect and co-ordinate the medical work of the various Mediterranean Commands and Expeditionary Forces on behave of the Director-General, A.M.S. back at the War Office. He also arranged for the reception of the sick and wounded from the Dardanelles to Egypt and Malta, and equitably distributed personnel to the three Commands, as well as tendered advise with regards to sanitation and co-operated with the Q.M.G�s branch of the staff and the Naval Transport officer for the working of the hospital ships. From October 1915, however, the Naval Transport officer�s post ceased to exist, resulting in William taking general control of the hospital ships based in Alexandria, running them under the authority of the General Officer Commanding the Levant Base, which had been established in Egypt for supplying and reinforcing the Dardanelles and Salonika armies. On 10th March 1916 he was recalled for duty at the War Office, and the appointment of a P.D.M.S., Mediterranean ceased to exist.
He arrived at the War Office on 18th March 1916. His new role, as Director of Medical Services, was to make inspections in the United Kingdom on behalf of the Director-General in connection with the methods employed by recruiting boards in different command areas. From February 1917 to March 1918 he oversaw the appointment of Assistant Director-General, A.M.S. after Lt/Col Blenkinsop vacated the appointment to transfer to the Mesopotamia Expeditionary Force. On the 1st March 1918, he was appointed Inspector of Medical Services with the rank of Lieutenant-General, a position he held until he retired on 7th May 1919. During 1919 he was made a Knight Commander of the Order of the Bath. William was the eldest Son the Provost of Dunbarton, John Babtie JP; and the husband of Edith Mary, daughter of W H Barry of Ballyadam, Co Cork.