The first blaze at the Magpie Cafe on Pier Street took six hours to put out after flames engulfed the roof on Saturday night.
A second fire broke out at about 15:30 BST but has since been brought under control.
The first is thought to have broken out in the top floor men's toilets. It is not yet clear what caused the second.
No-one was hurt in either incident and the restaurant is expected to close for several weeks.
Its owner, Ian Robson, earlier told the BBC it had been "a long night".
"We don't really know what started it, just that there was smoke in the gents' toilets on the top floor," he added.
The building is said to date back to 1750 when it was a Merchants House. It was used as a shipping office and by whaling crews before being converted into a cafe in 1939.
The famed restaurant has been reviewed by food critics and chefs, including Jay Rayner and Rick Stein.
A fire service spokesperson said an investigation is under way into the cause of the fire.
A famous fish and chip restaurant in Whitby has suffered two fires in 24 hours.