The college was founded on the original site of the 13th century Hospital of St John in Cambridge at the suggestion of John Fisher, Bishop of Rochester and chaplain to Lady Margaret. However, Lady Margaret died without having mentioned the foundation of St John's in her will and testament and it was largely the work of John Fisher which ensured that the college was founded. He had to obtain the approval of King Henry VIII of England, the Pope through an intermediary Polydore Vergil, and the Bishop of Ely to suppress the religious hospital and move ahead with its conversion to a college. Nevertheless the college received its charter on 9th April 1511. Further complications arose in obtaining money from the estate of Lady Margaret to pay for the foundation and it was not until 22 October 1512 that a codicil was obtained in the court of the Archbishop of Canterbury. In November 1512 the court of Chancery allowed Lady Margaret's executors to pay for the foundation of the college from her estates.
First Court was converted from the original hospital on the foundation of the college. It has since been gradually changed until finally the original 13th century hospital chapel and other buildings were demolished in the middle of the 19th century. The new chapel was designed by Sir George Gilbert Scott and includes in its interior some pieces saved from the original chapel. The original chapel foundations can still be seen in First Court. First Court was used as a prison in 1643 during the English Civil War, when the college was on the Royalist side, while the city of Cambridge was largely on the Parliamentary side.
Second Court, built from 1589-99, has been described as 'the finest Tudor court in England'. Reputedly under the Oriel window in the north range of the court the treaty between England and France which established the marriage of King Charles I of England to Queen Henrietta Maria. Now the Combination Room, but before the 19th century part of the Master's Lodge, the first-floor gallery along the north range has the largest single ceiling in Cambridge.
The Old Library was built in 1624, largely with funds donated by John Williams, Bishop of Lincoln. It includes a very fine bay window overlooking the River Cam which has the letters ILCS on it, standing for Iohannes Lincolniensis Custos Sigilli, or 'John of Lincoln, Keeper of the Seal'. The remaining parts of Third Court were added in 1669-72.
Connecting Third court to New Court is New Bridge, more commonly known as the Bridge of Sighs. It is named after the Bridge of Sighs in Venice which it resembles. The other bridge over the river, the Kitchen Bridge (named after the lane it followed the line of, Kitchen Lane) which is to the south of the Bridge of Sighs was partly based on plans made by Sir Christopher Wren.
The 19th-century Gothic New Court, probably one of the most famous buildings in Cambridge, was the first College buildnig on the West Side of the River. It was built mainly as a result of the need to accommodate the increased numbers of students.
The School of Pythagoras, built in c1200AD is built on land which was owned by Merton College, Oxford until 1959. It predates any of the other buildings in the College, although it was originally a private house, rather than part of the college.