John Cook was born on April 13, 1805, in Dumfriesshire, Scotland.

He was a clergyman, educated at Glasgow and Edinburgh Universities. In 1835, he was ordained a priest of the Presbyterian Church of Scotland and in 1836, he came to Canada where he obtained a position at St. Andrew's Church in Quebec City. As its minister for many years, he played a prominent part in bringing about the union of Presbyterians in Canada in 1875. He participated in the Quebec Charitable Firewood Society, a Protestant anglophone body that bought firewood in summer at low prices for winter distribution to the destitute. In 1845, he helped organize a major relief effort for the victims of the fires in the suburbs of Saint-Roch and Saint-Jean. In 1848, he published "The Advantages of Life Assurance to the Working Classes". In 1860, he was appointed a commissioner responsible for foundlings and indigent sick in the district of Quebec. He was a member of the Quebec Library Association, the St Andrew’s Society, and the Quebec Bible Society. Cook was deeply committed to promoting education. He was one of the founders of Queen's University, Kingston, and was its principal in 1857-1858. In 1861, he was appointed principal of Morrin College, Quebec and he retained this position until his death. Cook was also a member of the Board of Governors of McGill College. In 1880, the degree of LL.D. was conferred on him by Queen's University, Kingston.

About 1837 he married Eliza Airth (1805-1881). He died on March 31, 1892, in Quebec City, Quebec.