In 1167 Henry II ordered all English students on the Continent to return to England. Many of these students decided to settle in Oxford in an attempt to create the kind of university they had seen in Europe. Disputes between the students and residents led to riots. Some of these students fled to Cambridge where they established a new university. The loss of Oxford's students hurt the local economy and in 1214 traders and merchants invited them back again.

University College was founded in 1249 by William of Durham. Balliol was established in 1263 and Merton, the first residential college, arrived the following year. Merton set the collegiate pattern which became standard in both Oxford and Cambridge. These colleges were self-governing institutions in which teachers and students lived together as a community. Fourteen other colleges were founded by the end of the 16th century: St Edmund Hall (1278), Exeter (1314), Oriel (1326), Queen's (1340), New (1379), Lincoln (1427), All Souls (1438), Magdalen (1458), Brasenose (1509), Corpus Christi (1517), Christ Church (1546), Trinity (1554), St John's (1555) and Jesus (1571)

Four more colleges were established in the 19th century for women: Lady Margaret Hall (1878), Somerville (1879), St. Hugh's (1886) and St. Hilda's (1893). Other Oxford colleges include St. Anne's (1879), Mansfield (1886), St. Benet's (1897), Blackfriars (1921), St. Peter's (1929), Nuffield (1937), Linacre (1962) and St. Catherine's (1963).

Oxford University was first granted the right to have two MPs in 1613. The vote was given to proctors and all living masters of arts of the university, wherever they lived. The two Tory candidates were almost always guaranteed success. Around 1,300 people voted in elections. Between 1817 and 1829 one of Cambridge's two MPs was Sir Robert Peel. However, Peel's support for Catholic Emancipation made him unpopular in Oxford and he was defeated by 146 votes in February 1829.