The church at Charlton is thought to date back at least 800 years, possibly more. It is picturesque, with a turret tower and a sundial over the porch. There is a chancel with north chapel and south vestry. These seem to date from the late 12th century. In the 14th century the aisle was extended and the tower built. In the late 16th century a large window was inserted in the nave. It is to be found on Park Street, near one of the entrances to Charlton Park. The earliest reference to it being dedicated to St. John the Baptist was probably 1763. The registers are complete from 1661 and, other than those in current use, are held in the Wiltshire & Swindon History Centre at Chippenham.
The records of Malmesbury Abbey show there was a chapel in Charlton in the 13th century- this probably became the church. The lands at Charlton belonging to Malmesbury Abbey were bought by William Stumpe at the time of the dissolution; his descendents became the owners of Charlton Park and the Earls of Suffolk.
There is an oak panel carved with a lion and unicorn above the pulpit and this is thought to have been made in the 17th century. A larger oak panel screens the organ and is carved with ten faces. The earliest remaining feature is probably a dedication cross found at the north east corner of the east wall. There is a niche above the door from the porch which once held a statue of some kind; probably either of St. John the Baptist or the Virgin Mary.