New Alresford was founded by the Bishop of Winchester, gaining its market charter in 1200. The settlement and the church predated the new town.
The entry for Alresford in the Domesday Survey of 1086 records the existence of three churches. These probably belonged to Old Alresford, New Alresford and Medstead. However, the oldest surviving element of the fabric of St John’s is a 13thc. lancet at the W end of the S aisle.
The church was remodelled in a Perpendicular style in the 14thc. It was badly damaged by a fire which destroyed much of the town in 1689. This left just the lower stages of the W tower and the outer walls standing. The church had been reconstructed, with wooden arcades, by 1694.
A vestry designed by W. H. Hunt was added to the S side of the chancel in 1857. At the same time new pews were installed in the nave and those in the galleries were rearranged. The galleries were lit by dormer windows.
The church was largely rebuilt in a Perpendicular style in 1896-98 by Sir Arthur Blomfield, the Diocesan architect. The chancel was extended, the nave arcades rebuilt, the galleries removed, the aisles lowered, and the main entrance moved from N to W. During this work the font fragment was discovered.
The church hall was built to the SE, to designs by K. G. Brooks, in 1967-68.