The town name is of Old English origin. Excavations in the town centre in 1985 found an Iron Age hillfort dating from around 650BC. The town is sited on an outcrop of Portlandian limestone which accounts for its prominent position in the surrounding landscape, which is largely clay. Aylesbury was a major market town in Anglo-Saxon times, famous in addition as the burial place of Saint Osyth, whose shrine attracted pilgrims. The Early English parish church of St. Mary (with many later additions) may be built over the remains of a Saxon crypt. At the Conquest, the king took the manor of Aylesbury for himself, and it is listed as a royal manor in the Domesday Book, 1086.In 1450 a religious institution called the Guild of St Mary was founded in Aylesbury by John Kemp, Archbishop of York. Known popularly as the Guild of Our Lady it became a meeting place for local dignitaries and a hotbed of political intrigue. The Guild was influential in the final outcome of the Wars of the Roses. Its premises at the Chantry in Church Street, Aylesbury, are still there, though today the site is occupied mainly by almshouses.

Aylesbury was declared the county town of Buckinghamshire in 1529 by King Henry VIII: Aylesbury Manor was among the many properties belonging to Thomas Boleyn the father of Anne Boleyn and it is rumoured that the change was made by the king in order to curry favour with the holders of the manor. (Previously the county town of Buckinghamshire was Buckingham).The town played a large part in the English Civil War when it became a stronghold for the Parliamentarian forces, like many market towns a nursing-ground of Puritan sentiment. Its proximity to Great Hampden, home of John Hampden has made of Hampden a local hero: his silhouette is on the emblem used by Aylesbury Vale District Council and his statue stands prominently in the town centre. Aylesbury born composer, Rutland Boughton (1878-1960), possibly inspired by the statue of John Hampden, created a symphony based on Oliver Cromwell.

The Jacobean mansion of Hartwell nearby was the residence of Louis XVIII during his exile (1810 – 1814). Bourbon Street in Aylesbury is named after the King. Louis's wife, Marie Josephine of Savoy died at Hartwell in 1810 and is buried in the churchyard there. She is the only French Queen to be buried on English soil. The town's heraldic crest is the Aylesbury duck, which has been bred here since the birth of the Industrial Revolution.

A notable institution is Aylesbury Grammar School, which was founded in 1598; other grammar schools now include Sir Henry Floyd Grammar School and Aylesbury High School. Other notable buildings are the King's Head Inn, which with the Fleece Inn at Bretforton is one of the few public houses in the country owned by the National Trust still run as a public house, and the Queens Park Centre, the UK's largest independent arts centre.Chequers, the country residence of the Prime Minister of the United Kingdom since 1921, is just south-east of Aylesbury.James Henry Govier the British painter and etcher resided at Aylesbury and produced a number of works relating to the town including the church, canal, Walton, Aylesbury Gaol, The King's Head and views of the town during the 1940s and 1950s, examples of which can be seen in the county museum in Aylesbury. Govier was born at Oakley, and was the etching demonstrator at The Royal College of Art.