The parish used to be part of the manor of Headington. The first mention of a church at Marston is in a charter of 1122 by which the chapel of Marston was granted to the Augustinian canons of St Frideswide's. The present church of St Nicholas dates from the 12th century, with substantial additions in the 15th.
The village played an important part in the Civil War, during the siege of Oxford. While the Royalist forces were besieged in the city, which had been used by King Charles I as his capital, the Parliamentary forces under Sir Thomas Fairfax had their headquarters in Marston, and used the church tower as a lookout post for viewing the enemy's artillery positions in what is now the University Park.
During the 20th century expansion of Oxford, new housing followed the road from St Clements towards Marston, which was soon swallowed up by the city. New Marston became a separate parish in the 1950's.