The son of James Bonar, Solicitor of Excise for Scotland, he was born and educated in Edinburgh. He comes from a long line of ministers who have served a total of 364 years in the Church of Scotland. One of eleven children, his brothers John James and Andrew Alexander were also ministers of the Free Church of Scotland. He had married Jane Catherine Lundie in 1843 and five of their young children died in succession. Towards the end of their lives, one of their surviving daughters was left a widow with five small children and she returned to live with her parents. Bonar's wife, Jane, died in 1884. He is buried in the Canongate Kirkyard.

In 1853 Bonar earned the Doctor of Divinity degree at the University of Aberdeen.

He entered the Ministry of the Church of Scotland. At first he was put in charge of mission work at St. John's parish in Leith and settled at Kelso. He joined the Free Church at the time of the Disruption of 1843, and in 1867 was moved to Edinburgh to take over the Chalmers Memorial Church (named after his teacher at college, Dr. Thomas Chalmers). In 1883, he was elected Moderator of the General Assembly of the Church of Scotland.

He was a voluminous and highly popular author. He also served as the editor for "The Quarterly journal of Prophecy" from 1848 to 1873 and for the "Christian Treasury" from 1859 to 1879. In addition to many books and tracts wrote a number of hymns, many of which, e.g., "I heard the voice of Jesus say" and "Blessing and Honor and Glory and Power," became known all over the English-speaking world. A selection of these was published as Hymns of Faith and Hope (3 series). His last volume of poetry was My Old Letters. Bonar was also author of several biographies of ministers he had known, including "The Life of the Rev. John Milne of Perth" in 1869, - and in 1884 "The Life and Works of the Rev. G. T. Dodds", who had been married to Bonar's daughter and who had died in 1882 while serving as a missionary in France.

His hymns include:

• Fill thou my life, O Lord, my God
• I heard the Voice of Jesus say
• Thy way, not mine, O Lord
• Here, O my Lord, I see Thee face to face
• A few more years shall roll
• Come Lord and tarry not

Some of his books include:

• God's Way of Peace ISBN 1459096304
• Follow the Lamb ISBN 0906731631
• Light & Truth: Bible Thoughts and Themes on The Acts & Larger Epistles - commentary on Acts, Romans, and 1 Corinthians and 2 Corinthians ASIN B002ZJRS9K
• Light & Truth: Bible Thoughts and Themes on Revelation] - commentary on the Book of Revelation ASIN B002ZRQ55U