St Margaret’s is dedicated to St Margaret of Scotland and is situated in woodland away from houses but close to the River Waveney; it stands at the north end of an historic causeway which in medieval times continued across the river and was a key crossing point from Suffolk to Norfolk. The church, listed Grade 2* and thought to date from Saxon times, is largely of 13th and 14th century construction, with a 15th century south porch funded by Alice, Duchess of Suffolk, bearing the arms of the de la Pole and Chaucer families. The porch has a small alms recess in the east wall and the door retains its 13th century ironwork including sanctuary handle.

The lower courses of the round tower are of local flint, with later additions and a brick crenellated top. The tower has a ground floor lancet window and four small slit windows at belfry level, all deemed 14th century. It contains three bells of 15th, 17th and 18th century origins which now ring with a chiming apparatus.

Unusually, the nave is lower than the chancel but marks on the tower indicate that the nave roof, now of slate, was once steeper and thatched. There are fragments of Saxon limestone at the base of the N W angle of the nave. The chancel roof is tiled.

The windows in the nave are 14th century Perpendicular but there are two 13th century lancet windows in the north wall of the chancel. The east window has Decorated tracery and Victorian stained glass. The floor of the nave and chancel aisles is of glazed tiles and the lower steps of the rood staircase are clearly visible.

There are a number of memorials in the chancel, including six floor slabs and two wall tablets: these largely memorialise the owners of Syleham Hall. In the nave, there is one slab at the west end and three wall tablets memorialise owners of Monks Hall and Syleham Manor. In 2014 a stone wall memorial was added to commemorate the dead of the two World Wars.

There is a small font, thought to be 14th century on an earlier base. The wardens' chest is 13th century banded with iron and with five locks. Other furnishings are of 17th century oak and there is a pipe organ, now with electric blower.

The churchyard is bounded by hedges and woodland, with gate and railings to the south east; it is a designated County Wildlife Site. There are three chest-tombs, two to the east of the church and one to the west of the south porch, one monument and numerous headstones. Yew trees guard the junction of the path from the chancel door with the path to the gate from the south porch.

St Margaret’s has one particular claim on history, as it was the site of the surrender by the rebel Earl Bigod to King Henry II in 1174: the Earl's castles of Bungay and Framingham were forfeited but he retained his head.  (See also: Why St Margaret of Scotland?)