The son of a clergyman, he grew up in Devon, where he developed an interest in nature study and geology. After graduating from Magdalene College, Cambridge, he was ordained in 1842 as curate of Eversley and two years later became parish priest there. Much influenced by the theologian Frederick Denison Maurice (Maurice, Frederick Denison), he became in 1848 a founding member of the Christian Socialist movement (Christian Socialism), which sought to correct the evils of industrialism through measures based on Christian ethics. His first novel, Yeast (printed in Fraser's Magazine, 1848; in book form, 1851), deals with the relations of the landed gentry to the rural poor. His second, the much superior Alton Locke (1850), is the story of a tailor-poet who rebels against the ignominy of sweated labour and becomes a leader of the Chartist movement. Kingsley advocated adult education, improved sanitation, and the growth of the cooperative movement, rather than political change, for the amelioration of social problems. The strenuous tone of his Broad Church Protestantism is often described as “muscular Christianity.” His novels, similarly, are often attributed to the “muscular” school of fiction.

Kingsley soon turned to writing popular historical novels. Hypatia (1853) is a luridly erotic story set in early Christian Egypt. Westward Ho! (1855) is an imperialist and anti-Roman Catholic adventure set in the Elizabethan period, and Hereward the Wake (1866) is about Anglo-Saxon England and the Norman Conquest, also with an anti-Catholic slant. Kingsley's fear of the trend within the church toward Roman Catholicism, growing out of the Oxford Movement, led to a notorious controversy with John Henry (later Cardinal) Newman (Newman, John Henry). In answer to an attack by Kingsley, Newman wrote his Apologia pro Vita Sua (1864), the history of his religious development.

The didactic children's fantasy The Water-Babies (1863) combines Kingsley's concern for sanitary reform with his interest in natural history and the theory of evolution. He was also a very competent poet who wrote some memorable ballads ( "Airly Beacon," "The Sands of Dee," "Young and Old" ). Kingsley became chaplain to Queen Victoria (1859), professor of modern history at Cambridge (1860–69), and canon of Westminster (1873). His brother Henry Kingsley (Kingsley, Henry) was a novelist, and his niece Mary Henrietta Kingsley (Kingsley, Mary Henrietta) was a travel writer and adventurer.