Lyell was the son of a notable botanist. He was born at Kinnordy in Scotland and educated at Oxford University, where he developed an interest in geology and attended the lectures of William Buckland. While a student at Oxford he made, in 1819, the first of his many geological trips to the Continent and he met Alexander von Humboldt and Georges Cuvier in France in 1823. He studied law and was called to the bar in 1825, but because of strained eyesight he turned increasingly to geological investigation.

During the following years Lyell traveled extensively on the Continent, his studies culminating in the publication of his three-volume masterpiece The Principles of Geology (1830–33). This was to be published in 11 editions in his lifetime and established him as a leading authority on geology. He became professor of geology at King's College, London (1831–33), but gave this up to continue his geological studies, traveling throughout Europe and visiting America in 1841 and 1845.

In Principles Lyell established the doctrine of uniformitarianism already stated by James Hutton and John Playfair and the first volume, published in 1830, was subtitled “Being an Attempt to Explain the Former Changes of the Earth's Surface by Reference to Causes now in Operation.” Lyell explicitly rejected the work of Abraham Werner, in which some unique deluge is the chief agent producing the Earth's topography. Uniformitarianism also involved the rejection of the catastrophism theory followed by zoologists such as Cuvier to explain dramatic changes in the flora and fauna of the Earth. Instead Lyell saw the crust of the Earth as being shaped by forces operating over unlimited time.

Lyell contributed considerable knowledge and analysis to geology. In 1833 he introduced the structure of the Tertiary in which it spread from the Cretaceous to the emergence of man and was subdivided on the basis of the ratio of living to extinct species – Eocene, Miocene, Pliocene, and Pleistocene. His other works included Elements of Geology (1838) describing European rocks and fossils from the most recent to the oldest then known.

Charles Darwin, in his work Origin of Species (1859), drew heavily on Lyell's Principles. Lyell did not at first share Darwin's views and it was not until the tenth edition of the Principles (1867–68) that he expressed any support for evolutionary theory. Even then in his The Antiquity of Man (1863), which was published in four editions before 1873, Lyell denied that the theory could be applied to man.

Lyell was knighted in 1848 and created a baron in 1864. He became president of the British Association in 1864.