A mediaeval chapel existed on the tip of the Sciberras peninsula before the arrival of the Order of St John in Malta.

The chapel's existence was documented in 1488 and was later integrated within Fort St Elmo when the fort was built in 1552.

The present church of St Anne is a small, single-celled building with a narrow façade restricted by the fortification walls. Its origins date back to the late mediaeval period.

The chapel is roofed by a fine barrel vault and coffered ceiling. The internal walls of the chapel are plain with a single arched recess in the north wall. The altar is set within an arched alcove richly decorated by sculptures. The coat-of-arms of Grandmaster Lascaris is displayed above the altar.

The chapel suffered extensive damage during the Great Siege of 1565, but it was repaired and restored by Grand Master Lascaris.

Mepa scheduled the church of St Anne as a Grade 1 national monument as per Government Notice No. 276/08 in the Government Gazette dated March 28, 2008 and as part of Fort St Elmo as per Government Notice No. 133/01 in the Government Gazette dated February 9, 2001.