The village name 'Marston' is Anglo Saxon in origin, and means 'marsh farm'. The prefix 'Fleet' refers to a stream in the parish, and was added to distinguish the village from nearby North Marston. In the Domesday Book of 1086 the village was recorded as Mersetune.
At one time a railway line ran through the parish though this has long since been dismantled. All that remains of the village today is a small number of houses and a farm, and the parish church of St Mary the Virgin.