In 1888 the Very Rev.Professor A.H.Charteris laid before the General Assembly his scheme for the organisation of women's work in the Church. The scheme was to include the Women's Guild and the Order of Deaconesses. His scheme having been approved, Professor Charteris acquired the house in the Pleasance that had once belonged to Lord Carnegie. On this site he proposed to found institutions for the training of Deaconesses for missionary work both at home and abroad.

In 1889 St.Ninian's Mission opened. It provided practical training in mission work among the overcrowded tenements of the Pleasance, the Cowgate and the adjacent closes.

The Deaconess Hospital was opened in 1894 in a building next to St.Ninian's Mission. It provided practical training in nursing for Deaconesses, each of whom spent a year there as part of her training. Deaconesses who wished to become fully qualified nurses spent a further three years in the hospital's Nurses' Training School.

In 1912 as a tribute to Professor Charteris the Charteris Memorial Church was opened next to his two foundations.

Although the hospital's primary purpose was to provide a training school for missionary Deaconesses, it also provided a much needed medical service to the local community in one of the poorest districts of the City.

The original hospital had 24 beds. Extensions in 1897 and 1912 brought this total up to 42. Emergency beds added during World War 1 further increased the number to 68, but these were reduced after 1918, so that in 1920 there were 50 beds including "open-air" beds and children's cots. There were five wards: Charteris, named after the hospital's founder; Houldsworth, named after the Misses Houldsworth of Ayr who were generous subscribers; the Children's Ward which had 18 beds, six of which were on the balcony; Deaconess for church workers; and Moray. There was also a busy out-patient department.

In 1934 the hospital was closed allow for a major reconstruction. The site was extended by the purchase of the adjoining Police Station and of old buildings to the rear. A new hospital block was built, named Lord Sande Memorial Wing after Lord Sande, for many years Chairman of the hospital's Board of Management. The hospital was re-opened on 1st December 1936 by the Duke and Duchess of York, the Children's Ward being renamed the Princess Elizabeth Children's Ward in memory of the occasion. One of the wards in the new wing was named the Women's Guild Ward to commemorate the large endowment by that organisation.

In addition to the general hospital functions, the Deaconess provided a home visiting or District service. A regular system of instruction in District Nursing and Midwifery was carried out by the staff nurse in charge of District work.

In 1948, with the introduction of the National Health Service, the Deaconess became part of Edinburgh Southern Hospitals group of South Eastern Regional Hospital Board. In 1974 it came under the South Lothian District of Lothian Health Board, and in 1984 it joined the Royal Infirmary of Edinburgh and Associated Hospitals Unit. In 1990 the Deaconess Hospital Closed, and Deaconess House is now the home of Lothian Health.