The original church tower was erected in 1845 but developed a lean, was deemed unsafe and was dismantled in 1864. The present tower was designed by Edmund Blacket and erected during the period 1865–1870. Sandstone for the tower's window mouldings was hauled by bullock from the Camden-Bargo district, a distance of . The spire was completed in 1877, making the church on a hill a prominent countryside landmark. The tall trees, many planted by long-serving Rector of Canberra Revd Pierce Galliard Smith, formed another landmark. The church and associated schoolhouse museum were added to the (now defunct) Australian Register of the National Estate on 21 October 1980. The church, churchyard and Schoolhouse Museum are now listed by the ACT Heritage Council, which notes, in particular, that the east and west lychgates at St John's are a rare example of this type of structure in Australia. Memorial plaques to parishioners cover the interior of the nave, from earlier pastoral families to eminent Australians after Australia's federation. Prominent memorials include those for Sir Robert Garran, Sir Littleton Groom, H. V. Evatt, Sir William McKell, Major General Sir William Bridges and General Sir Brudenell White. Extensive use of stained glass is evident in the chancel, the nave and within the tower. The chancel's east window was added between 1872 and 1874, and depicts biblical scenes related to Saint John the Baptist, after whom the church is dedicated. The east window was designed by William Macleod and made by the Sydney firm of John Falconer. It is one of the earliest Australian stained glass windows and was a prize-winning window at the Sydney Exhibition in 1973 before its installation at the church. The Royal Military College and St John's have long been associated with each other. Both are situated on land originally owned by Campbell. The historical ties between the church and the college are recognised by the military colours (flags) which are "laid up" beneath the organ gallery: one of the Werriwa Regiment and the other of the Royal Military College. In the side chapel on the north edge is a small bamboo cross with the words "Reconciliation and Repentance". The cross was presented to the church by the presiding bishop of the Anglican Church in Japan, Bishop Michael Yashiro, on 9 June 1950 in the years following the Second World War. It serves as a memorial to Sister May Hayman, a staff member at the Canberra Hospital and a parishioner at St John's.