In March 1942, as a Captain in command of number 6 Troop, No. 2 Commando, he [Micky Burn] took part in Operation Chariot, the St. Nazaire Raid, his own 6 Troop contributing 29 men to the overall total of 264 Army personnel taking part. As leader of the starboard column of troop carried in several Motor Launches (MLs), Burn's ML192 was one of the first vessels to come under fire, crashing ablaze into the Old Mole. Of his 6 Troop contingent, 14 men were killed. The rest, many of whom were forced to take to the water, were captured early on.

Having been hauled ashore by one of his men, and despite being wounded several times, Burn was able to make his way to his target, the only member of his team to do so. Burn later attempted to escape the tightening German cordon along with two of his men, one of whom was killed. Burn, along with his remaining companion, was captured and entered a lengthy period of confinement as a "guest of the Reich".

For his actions during the raid Burn received the award of the Military Cross. Of the 609 soldiers and sailors who entered the Loire estuary that night, five were awarded the Victoria Cross – the greatest number for any single action during the war.