The ancient village of Clayton, situated where the main route from London to Brighton crossed an east–west track at the foot of the South Downs, existed at the time of the Domesday survey in 1086, when it was called Claitune or Claitona.
 It was at the southern end of the parish of the same name, which covered 1,414 acres (572 ha) of mostly rural land running north (and downhill) from the summit of the South Downs.
 The manor of Clayton was held at that time by William de Watevile for William de Warenne, who built the nearby Lewes Castle.
 The church was in the possession of Lewes Priory, which had been given it by de Warenne in 1093.
 The manor and church in the neighbouring parish of Keymer had the same ownership.
 The original dedication of St John the Baptist's Church was All Saints—a common dedication during the Anglo-Saxon era.

The standard layout of Anglo-Saxon churches was a tall nave without aisles linked to a smaller, square-ended (not apsidal) chancel by a chancel arch.
 St John the Baptist's Church follows this form; and the nave and chancel arch, along with parts of the north and south chancel walls, survive from the 11th century.
 On the north side of the nave, fragmentary remains of a 12th-century porticus (a low side chapel, similar to a transept) can be seen: on the inside, there is a blocked round-headed opening, while on the outside a roofline is visible.
 A similar porticus of the 13th century existed on the south side; its remnants can still be seen.

The entrance porch on the north wall was erected in the 15th century, but the heavy oak door dates from the Norman era.
 The entrance was originally on the south side; suggested reasons for its move include avoiding the prevailing wind, which blows off the hills straight into the south wall, or a change in the location of the nearby road in medieval times.
 The squat wooden belfry at the west end of the nave is also 15th-century, as are two of the three bells.
 The path leading to the porch is unusually made of "ripplestone"—Horsham sandstone taken from a nearby riverbed.

The chancel was rebuilt in the 19th century, and a vestry was added on the northwest side.
 Minor restoration work was carried out in the 20th century.
 A blocked window, discovered in the north wall of the chancel, was found be an original Anglo-Saxon window.
 The former side-chapel on the north side was discovered during excavation work in 1918.
 The lychgate at the entrance to the churchyard was built in the early 1920s by Philip Mainwaring Johnston and serves as Clayton's war memorial.
A Falklands War casualty is commemorated, and there is also a military grave from that conflict in the churchyard, where American theatrical producer Marc Klaw is also buried.
To commemorate the Millennium, new stained glass was inserted in the west window of the nave; the design received considerable praise.
The ancient village of Clayton, situated where the main route from London to Brighton crossed an east–west track at the foot of the South Downs, existed at the time of the Domesday survey in 1086, when it was called Claitune or Claitona.  It was at the southern end of the parish of the same name, which covered 1,414 acres (572 ha) of mostly rural land running north (and downhill) from the summit of the South Downs.  The manor of Clayton was held at that time by William de Watevile for William de Warenne, who built the nearby Lewes Castle.  The church was in the possession of Lewes Priory, which had been given it by de Warenne in 1093.  The manor and church in the neighbouring parish of Keymer had the same ownership.  The original dedication of St John the Baptist's Church was All Saints—a common dedication during the Anglo-Saxon era.
The standard layout of Anglo-Saxon churches was a tall nave without aisles linked to a smaller, square-ended (not apsidal) chancel by a chancel arch.  St John the Baptist's Church follows this form; and the nave and chancel arch, along with parts of the north and south chancel walls, survive from the 11th century.  On the north side of the nave, fragmentary remains of a 12th-century porticus (a low side chapel, similar to a transept) can be seen: on the inside, there is a blocked round-headed opening, while on the outside a roofline is visible.  A similar porticus of the 13th century existed on the south side; its remnants can still be seen.
The entrance porch on the north wall was erected in the 15th century, but the heavy oak door dates from the Norman era.  The entrance was originally on the south side; suggested reasons for its move include avoiding the prevailing wind, which blows off the hills straight into the south wall, or a change in the location of the nearby road in medieval times.  The squat wooden belfry at the west end of the nave is also 15th-century, as are two of the three bells.  The path leading to the porch is unusually made of "ripplestone"—Horsham sandstone taken from a nearby riverbed.
The chancel was rebuilt in the 19th century, and a vestry was added on the northwest side.  Minor restoration work was carried out in the 20th century.  A blocked window, discovered in the north wall of the chancel, was found be an original Anglo-Saxon window.  The former side-chapel on the north side was discovered during excavation work in 1918.  The lychgate at the entrance to the churchyard was built in the early 1920s by Philip Mainwaring Johnston and serves as Clayton's war memorial. A Falklands War casualty is commemorated, and there is also a military grave from that conflict in the churchyard, where American theatrical producer Marc Klaw is also buried. To commemorate the Millennium, new stained glass was inserted in the west window of the nave; the design received considerable praise.
St John the Baptist's Church, Clayton