Magnus, having reigned for less than three years, becomes ill and dies in Nidaros (Trondheim) on April 28, 1069.

The sagas posit that Magnus died of ringworm, but modern scholars have proposed that he instead may have died of ergotism (poisoning by the Claviceps purpurea fungus).

Snorri Sturluson writes briefly in the Saga of Harald Hardrade that Magnus was "an amiable king and bewailed by the people."

Magnus's kingship has been downplayed in later history partly due to his short tenure, and because most of it was together with his brother.

The subsequently long reign of Olaf also contributes to overshadow Magnus's reign, combined with the fact that the later Norwegian royal dynasties only descend (or claimed descent) from Olaf.

The king known today as Magnus VI of Norway (the first Norwegian king known to use regnal numbers) originally used the regnal number IV for himself in contemporary Latin letters, leaving out Magnus Haraldsson.

As the numbering system has seen changes in modern times, Magnus Haraldsson is today included as Magnus II.