The church is dedicated to St Magnus the Martyr, earl of Orkney, who died on 16 April 1118. He was executed on the island of Egilsay having been captured during a power struggle with his cousin, a political rival. Magnus had a reputation for piety and gentleness and was canonised in 1135.
The identity of the St Magnus referred to in the church's dedication was only confirmed by the Bishop of London in 1926. Following this decision a patronal festival service was held on 16 April 1926. In the 13th century the patronage was attributed to one of the several saints by the name of Magnus who share a feast day on 19 August, probably St Magnus of Anagni (bishop and martyr, who was slain in the persecution of the Emperor Decius in the middle of the 3rd century). However, by the early 18th century it was suggested that the church was either "dedicated to the memory of St Magnus or Magnes, who suffer'd under the Emperor Aurelian in 276 [see St Mammes of Caesarea, feast day 17 August], or else to a person of that name, who was the famous Apostle or Bishop of the Orcades." For the next century historians followed the suggestion that the church was dedicated to the Roman saint of Cæsarea. The famous Danish archaeologist Professor Jens Jacob Asmussen Worsaae (1821–85) promoted the attribution to St Magnus of Orkney during his visit to the British Isles in 1846-7, when he was formulating the concept of the 'Viking Age', and a history of London written in 1901 concluded that "the Danes, on their second invasion ... added at least two churches with Danish names, Olaf and Magnus". A guide to the City Churches published in 1917 reverted to the view that St Magnus was dedicated to a martyr of the third century, but the discovery of St Magnus of Orkney's relics in 1919 renewed interest in a Scandinavian patron and this connection was encouraged by the Rector who arrived in 1921.