Owen was born in Lancaster in 1804, one of six children of a West Indian Merchant named Richard Owen (1754–1809). His mother, Catherine Longworth (nee Parrin), was descended from Huguenots and he was educated at Lancaster Royal Grammar School. In 1820, he was apprenticed to a local surgeon and apothecary and, in 1824, he proceeded as a medical student to the University of Edinburgh. He left the university in the following year and completed his medical course in St Bartholomew's Hospital, London, where he came under the influence of the eminent surgeon John Abernethy.
In July 1835 Owen married Caroline Amelia Clift in St Pancras by whom he had one son, William Owen. He outlived both wife and son. After his death, in 1892, he was survived by his three grandchildren and daughter-in-law Emily Owen, to whom he left much of his £33,000 fortune.
Upon completing his education, he contemplated the usual professional career, but his bent was evidently in the direction of anatomical research. He was induced by Abernethy to accept the position of assistant to William Clift, conservator of the museum of the Royal College of Surgeons. This congenial occupation soon led him to abandon his intention of medical practice and his life thenceforth was devoted to purely scientific labours. He prepared an important series of catalogues of the Hunterian Collection, in the Royal College of Surgeons and, in the course of this work, he acquired the unrivalled knowledge of comparative anatomy that enabled him to enrich all departments of the science and especially facilitated his researches on the remains of extinct animals.
In 1836, Owen was appointed Hunterian professor, in the Royal College of Surgeons and, in 1849, he succeeded Clift as conservator. He held the latter office until 1856, when he became superintendent of the natural history department of the British Museum. He then devoted much of his energies to a great scheme for a National Museum of Natural History, which eventually resulted in the removal of the natural history collections of the British Museum to a new building at South Kensington: the British Museum (Natural History) (now the Natural History Museum). He retained office until the completion of this work, in December, 1883, when he was made a knight of the Order of the Bath. He lived quietly in retirement at Sheen Lodge, Richmond Park, until his death in 1892.
His career was tainted by accusations that he failed to give credit to the work of others and even tried to appropriate it in his own name. This came to a head in 1846, when he was awarded the Royal Medal for a paper he had written on belemnites. Owen had failed to acknowledge that the belemnite had been discovered by Chaning Pearce, an amateur biologist, four years earlier. As a result of the ensuing scandal, he was voted off the councils of the Zoological Society and the Royal Society.
Owen always tended to support orthodox men of science and the status quo. The royal family presented him with the cottage in Richmond Park and Robert Peel put him on the Civil List. In 1843, he was elected a foreign member of the Royal Swedish Academy of Sciences.
He died at home on 15 December 1892 and is buried in the churchyard at Ham near Richmond, Surrey.