Around 1480, Franciscan Friars had followed the Spanish armies to Gibraltar and as well as looking after the people they began to build a Friary. The Church was finished in 1535, richly decorated in red and gold, it formed the North side of the Friary, which was build around a shady courtyard, with a cloister where the friars could walk and read. Their church was the first to be built on the rock.

The Franciscan Friars stayed on in Gibraltar until just before the thirteenth Siege began in 1727, after the siege a year later, the governor took their Friary, which was the best building on the rock, as his residence. The Franciscan Chapel was then taken over from the Roman Catholic obedience by the Church of England, and it became the governor's private chapel, although it was also used by the Officers of the Garrison and their families. The Church was now renamed "The King's Chapel".

In 1779, before the Great Siege began, General Elliot had all the landmarks of the rock demolished to make targeting more difficult for the enemy, among which were all the Church Bells including the King's Chapel Belfry. Although the General promised to restore the belfries at the end of the Great Siege, it was only after 216 years, in 1995, that the King's Chapel got its bell back.

During the Great Siege, 1779-1783, great damage was done to the town by Spanish bomb boats in the bay, and the West end of the Church, and the South transepts were destroyed. After the Siege was lifted the Eastern half of the Church was refurbished and went back into service as a Church again. The Western end and the South Transept were rebuild, but were incorporated into the Governors residence. Externally, the King's Chapel then was as you see it now.

By the 1820's, the custom was for the whole community to worship together, and the King's Chapel was too small. In 1834 a new Church was built ( the Holy Trinity), and the King's Chapel was closed. It only stayed closed for eight years as the new Church also became small.
Since 1842 the King's Chapel has been the main Church of the Army in Gibraltar.

During the Second World War the King's Chapel continued to operate as before, but there was no Chaplain permanently based in it, the Chaplains of the various army units shared the King's Chapel.

Sadly, in 1953, just after the King's Chapel had had a much needed post-war refurbishment, RFA Bedenham, an ammunition ship blew up in Gibraltar Harbour. Great damage was done to the buildings in the city, and the King's Chapel did not escape. All the stained glass windows went and the Nave ceiling, fortunately the rest of the Chapel survived. The Chapel had to be restored again and part of the new restoration was a beautiful North window depicting the late King George VI.

Today the King's Chapel is not just a historic building, it is a place were all Anglican service personnel now worship, as do Roman Catholics on Saturday evenings.