The ship is notable for a mutiny that occurred onboard whilst docked at Balboa, Panama in September 1944.

The ship's complement had swelled to 750 (instead of the normal 450) under the command of Rear Admiral Arthur George Talbot.

After reaching Balboa, Panama on 1 September 1944, an armed mutiny (the first in the Royal Navy since the 19th century) occurred on-board due to the atrocious conditions.

17 senior men were court-martialled and reduced in rank, whilst other mutineers were given six months' extra duties and punishment drill.

In February 1945 the Lothian became flagship to Rear Admiral Douglas Blake Fisher and operated as a control ship for merchant transports arriving to supply the British Pacific Fleet.