Pakenham is just under 5 miles E of the centre of Bury St Edmunds in rolling arable land. The village is just over half a mile long, running from Pakenham Manor in the W to the church at the E end. The village lies in the shallow valley that runs from Grimstone End in the N to Bartonmere in the S, and the church stands on a promontory overlooking the village.

St Mary's is a flint aisleless cruciform church with a central tower. The nave is 12thc., with Romanesque W and S doorways. The nave has N and S windows towards the E, both with plate tracery of the first half of the 13thc.; the W window is five-light Perpendicular. Only the E crossing arch is 12thc.; the other three are 19thc., as are both transepts. The N transept now houses the organ and lavatories, and the S was remodelled in 2002-03 as the Martin Room, a meeting area and kitchen funded by the Kristina Martin Trust. Both transepts date from the restoration of 1849-50 by S.S. Teulon, but the S stands on the site of an earlier transept. This had already been removed by 1822, but a drawing of that year shows its roofline. The chancel is 13thc., with plain lancets and 16thc three-light windows on the N and S walls, and a five-light 15thc. E window. There is a 19thc. N vestry. The tower is square in its lower part with added buttresses, and octagonal above. The bell-openings in the upper stage are 14thc., except for the S opening, which dates from 1958, and there is a battlemented parapet of brick, added c.1805. The W and S doorways and the E crossing arch contain Romanesque sculpture.

Land at Pakenham, Rougham and Barton was given in the will of Theodred, Bishop of London (942-51), to his kinsman Eadulf's son, Osgot. The Pakenham estate was given to St Edmunsbury Abbey by Edward the Confessor. In 1086 the estate included a church with 30 acres of free land in alms. In the reign of Henry I (1100-1135), one Walter founded a new church at Pakenham, and the 12thc. work recorded above belonged to Walter's church. In 1199, Abbot Sampson allocated one third of the demesne and tithes to St Saviour's Hospital, Bury, and in 1256 Abbot Walpole appropriated the church to the maintenance of hospitality in Bury. The vicar was allowed to retain the church manse and the land and tithes from it, together with other tithes and altar dues, but retained no income from crops. The abbot's manor house at Pakenham was one of 13 burnt by disaffected townsmen and tenants during the so-called Great Riot of 1327; a protest against the abbey's bad management of their estates and their alleged failure to meet their commitments. At the Dissolution the manor reverted to the crown, and in 1545 it was granted to Robert Spring of Lavenham and his son Thomas. It remained in the direct line until the death of Sir William Spring, fourth Baronet Pakenham, in 1735.

Benefice of Pakenham with Norton and Tostock.

The E crossing arch and doorways belong to Walter's church of 1100-35. The N and S doorways of St Mary's, Santon Downham, also have capitals with roll-moulded abaci and no imposts, and the S has the same arch profile as Pakenham too, but the capitals are trefoils and the nook-shafts decorated with cable. Santon Downham is 15 miles NW of Pakenham. Hunston provides a parallel for the missing S transept.