Sited by a steep-sided glen on a convenient fording point on the Water of Leith, Colinton's history dates back to before the 11th century.

Close to the Water of Leith is Colinton Parish Church, originally founded as the Church of Halis (Hailes) around 1095 by Elthelred, third son of Malcolm III and Queen Margaret. The nearby 15th century Colinton Castle, in the grounds of what is now Merchiston Castle School, was destroyed by Oliver Cromwell during his invasion of Scotland. Following repair, the castle was subsequently partially demolished by the artist Alexander Nasmyth in order to create a picturesque ruin.

Other notable figures with connections to Colinton include Robert Louis Stevenson who is known to have been a regular visitor to the village whose grandfather was also the Parish Minister in the Village, plus the philanthropist James Gillespie and architects Sir Robert Rowand Anderson and John James Burnet, who all lived in the village.

A number of innovative Arts and Crafts style cottages were also constructed in the village in the early 1900s by the architect Sir Robert Lorimer. Between 1909 and 1915, the War Office constructed Redford Barracks to the east of the village. The barracks represent the largest military installation built in Scotland since Fort George in the Highlands and they provide military accommodation, together with offices and training facilities.

The village was the location for numerous mills producing textiles, snuff, and paper. It is thought that the first banknotes produced by the Bank of Scotland were printed on paper manufactured in Colinton. The Caledonian Railway Company constructed a new spur line connecting Slateford and Balerno in 1874, which included the creation of a new station at Colinton. This line continued to carry passenger traffic until 1943, and finally closed when the carriage of freight was discontinued in the 1960s.