Kingsley was born in Holne, Devon, the second son of the Rev. Charles Kingsley and his wife Mary. His brother, Henry Kingsley, also became a novelist. He spent his childhood in Clovelly, Devon and Barnack, Northamptonshire and was educated at Helston Grammar School before studying at King's College London, and the University of Cambridge. Charles entered Magdalene College, Cambridge in 1838, and graduated in 1842. He chose to pursue a ministry in the church. From 1844, he was rector of Eversley in Hampshire, and in 1860, he was appointed Regius Professor of Modern History at the University of Cambridge.

In 1869 Kingsley resigned his professorship, and from 1870 to 1873 he was a canon of Chester Cathedral. While in Chester he founded the Chester Society for Natural Science, Literature and Art which played an important part in the establishment of the Grosvenor Museum. In 1872 he accepted the Presidency of the Birmingham and Midland Institute and became its 19th President. Kingsley died in 1875 and was buried in St Mary's Churchyard in Eversley.

Kingsley sat on the 1866 Jamaica Committee, along with John Bright, John Stuart Mill, Charles Darwin, Thomas Huxley, Thomas Hughes and Herbert Spencer, where he supported Jamaican Governor Edward Eyre's brutal suppression of the Morant Bay Rebellion.

One of his daughters, Mary St. Leger Kingsley (Mrs Harrison), became well known as a novelist under the pseudonym of "Lucas Malet".

Kingsley's life was written by his widow in 1877, entitled Charles Kingsley, his Letters and Memories of his Life.

Charles also received letters from Thomas Huxley in 1860 and later in 1863, discussing Huxley's early ideas on agnosticism.

Kingsley's interest in history is shown in several of his writings, including The Heroes (1856), a children's book about Greek mythology, and several historical novels, of which the best known are Hypatia (1853), Hereward the Wake (1865), and Westward Ho! (1855).

He was sympathetic to the idea of evolution, and was one of the first to praise Charles Darwin's book On the Origin of Species. He had been sent an advance review copy and in his response of 18 November 1859 (four days before the book went on sale) stated that he had "long since, from watching the crossing of domesticated animals and plants, learnt to disbelieve the dogma of the permanence of species." Darwin added an edited version of Kingsley's closing remarks to the next edition of his book, stating that "A celebrated author and divine has written to me that 'he has gradually learnt to see that it is just as noble a conception of the Deity to believe that He created a few original forms capable of self-development into other and needful forms, as to believe that He required a fresh act of creation to supply the voids caused by the action of His laws'." When a heated dispute lasting three years developed over human evolution, Kingsley gently satirised the debate as the Great Hippocampus Question.

His concern for social reform is illustrated in his great classic, The Water-Babies, A Fairy Tale for a Land Baby (1863), a kind of fairytale about a boy chimney sweep, which retained its popularity well into the 20th century. Furthermore in The Water-Babies he developed in this literary form something of a purgatory, which runs counter to his "Anti-Roman" theology. The story also mentions the main protagonists in the scientific debate over human origins, rearranging his earlier satire as the "great hippopotamus test". Kingsley was influenced by Frederick Denison Maurice, and was close to many Victorian thinkers and writers, for example the great Scottish writer George MacDonald.

As a novelist his chief power lay in his descriptive faculties. The descriptions of South American scenery in Westward Ho!, of the Egyptian desert in Hypatia, of the North Devon scenery in Two Years Ago, are brilliant; and the American scenery is even more vividly and more truthfully described when he had seen it only by the eye of his imagination than in his work At Last, which was written after he had visited the tropics. His sympathy with children taught him how to secure their interests. His version of the old Greek stories entitled The Heroes, and Water-babies and Madam How and Lady Why, in which he deals with popular natural history, take high rank among books for children.

Kingsley also wrote poetry and political articles, as well as several volumes of sermons. His argument, in print, with John Henry Newman, accusing him of untruthfulness and deceit, prompted the latter to write his Apologia Pro Vita Sua. He also wrote a preface to the 1859 edition of Henry Brooke's book The Fool of Quality in which he defends their shared belief in universal salvation.

Kingsley coined the term pteridomania in his 1855 book Glaucus, or the Wonders of the Shore.

Charles Kingsley's novel Westward Ho! led to the founding of a town by the same name—the only place name in England which contains an exclamation mark—and even inspired the construction of a railway, the Bideford, Westward Ho! and Appledore Railway. Few authors can have had such a significant effect upon the area which they eulogised. A hotel in Westward Ho! was named for him and it was also opened by him.

A hotel opened in 1897 in Bloomsbury, London, was named after Kingsley. It still exists, but changed name in 2001 to the Thistle Bloomsbury. The original reasons for the chosen name was that the hotel was opened by teetotallers who admired Kingsley for his political views and his ideas on social reform.