Ebenezer James MacRae was born on 18 January 1881, ‘a son of the manse’ in Clachan, Kilcalmonell, Argyll. His father was Alexander MacRae, a minister of the Free Church of Scotland and his mother was Annie Macrae, herself the daughter of another Free Kirk Minister. Somewhat surprisingly he was articled to the Roman Catholic Archibald Macpherson in 1899 and remained with him as draughtsman and assistant until December 1907. Macpherson, of whom he wrote in an affectionate memoir, was to remain a close friend for as long as he lived. During his time with Macpherson he studied at the School of Applied Art under Frank Worthington Simon from 1899 to 1904, concurrently attending Edinburgh University (1901-02) under Professor Gerald Baldwin Brown, and Heriot-Watt College (1901-07); from 1904 he attended the classes at the newly merged Edinburgh College of Art, including those in antique figure drawing, completing the course in 1906. During these early years he undertook sketching and measuring tours of York (1902 and 1904), Melrose (1904), Belgium (1905), Cambridge and Lincoln (1907) and Northamptonshire, Cambridge and Oxford (1907).

At the beginning of 1908 he moved to the office of John Kinross to spend six months assisting on his competition entry for the restoration of Kirkwall Cathedral, thereafter accepting a salaried post in the City Architect's Department under James Anderson Williamson. The following year, in collaboration with William Davidson who had been a fellow draughtsman in Macpherson's office, he exhibited designs for the furnishing and restoration of two Norfolk churches at the Royal Scottish Academy. Further collaborative designs were exhibited in 1911 and 1919, but the association between Davidson and MacRae appears to have been a loose one, as there is no evidence of a formal partnership having existed. He made additional tours of Paris in 1909, York in 1911, Norfolk in 1912 and Normandy in 1913. Surviving notes from this time show MacRae's interest in ecclesiastical architecture.

MacRae was admitted LRIBA in the mass intake of 20 July 1911, proposed by James Bow Dunn and the Edinburgh Architectural Association; but with characteristic determination he passed the qualifying exam in 1914 and was admitted ARIBA late that year, his proposers this time being Macpherson, John Watson, one of the teachers at the School of Applied Art and at Edinburgh College of Art and Alexander Lorne Campbell.

In the First World War MacRae served with the Royal Engineers. He returned to the City Architect's Office in 1918, becoming Depute City Architect at some time prior to 1925 and succeeding Williamson as City Architect in July of the latter year. He was admitted FRIBA in 1934, proposed by Thomas Forbes Maclennan. Later that year he and Wilson were members of the Department of Health fact-finding team led by the Permanent Secretary John Highton which toured the continental housing estates in Rotterdam, Amsterdam, Berlin, Frankfurt, Prague, Vienna and Paris. He compiled much of the analysis that appeared in the subsequent report which had a profound influence on local authority housing in the late 1930s.

MacRae was sympathetic to conservation, and would have perhaps reconditioned more buildings for housing if the subsidies available under the 1919 Act had continued. He renovated a number of Old Town buildings, like the Candlemakers Hall for club rooms, and where that was not practicable he rebuilt or retained several facades in something similar to their original form.  However, there were also several historic buildings demolished in his tenure, including tenements on the Canongate and Grassmarket, and those either side of the City Chambers removed for its extension.  The seventeenth century frontage of the Tailor's Hall complex on the Cowgate was a major loss.   Towards the end of his tenure he undertook a survey of the Old Town,  assisted by a newly qualified planner, William Dey, later of Gordon & Dey.  In 1945 and 1947 he produced policy reports on 'The Royal Mile', and followed this up with a another document, 'The Heritage of Greater Edinburgh', which listed all the traditional buildings in the city which were worthy of retention, very much in parallel with the Marquess of Bute's lists for the country as a whole.  It is useful to look at an earlier study of the Royal Mile undertaken around 40 years earlier by Bruce Home for the Old Edinburgh Club in 1908.   A large collection of related papers is preserved in Edinburgh Central Library. His interest also extended to historic statuary, and he published an essay on the 'Lead Equestrian Statue of Charles II' in the Book of the Old Edinburgh Club.  

MacRae retired in July 1946, but continued to be influential in a variety of fields, remaining a member of the RIAS Council until 1950. He had a particular interest in the Edinburgh Cripple and Invalid Children's Aid Society to which he gave generously of his time and money and was ornithologist, photographer and watercolourist, exhibiting at the RSA from 1915 until 1940. Several of the subjects record his travels in France c.1914 and Germany c.1930. John Ross McKay wrote of him that 'as an official he was easy of approach. His innate courtesy and charm of manner made it a pleasure to visit him...he was always ready to assist and never adopted the reserve of the official'.

He died on 15 January 1951 at the Deaconess hospital, Edinburgh, his home address then being Taprobane, Ratho., a house built for him.   His wiife, Dorothy Craigie, survived him.