John Baillie was born in 1886, the son of Rev John Baillie ( 1829-1891), Free Church minister at Gairloch, Ross & Cromarty in the north-west of Scotland, and his wife Annie Macpherson. John (senior) was a graduate of both the University of Edinburgh and Free Church College, Edinburgh

Following the death of his father in 1891, the family home was at Inverness and John (junior) was educated at Inverness Royal Academy and the University of Edinburgh. More study was undertaken at both the universities of Jena and Marburg and he held assistant positions at the University of Edinburgh before entering the church, as an assistant in 1912 and then being ordained in 1920.

The First World War saw Baillie playing an active role in both the YMCA and the British Expeditionary Force. The end of that war saw his marriage to Florence Jewel Fowler and the start of his academic career . He held a number of chairs at the Auburn and Union Theological Seminaries, New York, and at Emmanuel College, Toronto, but he eventually returned to Edinburgh to become Professor of Divinity at New College in 1934. The advent of the Second World War saw Baillie use the North American links he had maintained to help persuade US entry into the conflict. He was elected as Moderator of the General Assembly of the Church of Scotland and became Dean of the Faculty of Divinity at Edinburgh in 1950, holding this position until retrial six years later. As part of the ecumenical movement, John Baillie was member of both the British Council of Churches and the World Council of Churches; he became a President of the latter.