North Yorkshire Fire and Rescue Service said crews are already at the scene on Pier Road this afternoon (Monday May 1) and another five fire engines are en-route to the incident.
A North Yorkshire Fire service spokeswoman said: "There are flames coming from the roof."
Fire crews were called to the Magpie at 1.15pm last night to to deal with a blaze in the roof space.
A total of eight fire engines from the surrounding area attended last night's incident, included a high reach aerial ladder platform from Scarborough fire station and a crew from Middlesbrough.
Crews used breathing apparatus and fire fighting equipment to extinguish the fire. No people were injured as a result of the fire last night.
Fire investigation officers started an inspection of the premises at the time of the fire last night and the investigation was continuing today.
The Magpie has received hundreds of messages of support following last night's blaze.
The Magpie Cafe posted on its Facebook page this morning: "We can confirm, most importantly, everyone is okay and no one was hurt. Thank you to North Yorkshire Fire & Rescue Service and the emergency services for their assistance.
"We're down there now surveying the damage and will put out a statement when we know more. In the meantime, thank you all for your kind messages."
Messages of support for the restaurant, which is among Britain's top fish and chip eateries, have flooded in on social media.
Jayne Taylor said: "Shocked to see photo. Relieved no one injured. Hope you are soon up and running. We eat with you often when visiting Whitby, the food and service is always excellent. Best Wishes to all!"
While another diner, Sue Henshaw, said: "Our favourite place to eat when in Whitby once a year. I hope you can soon repair the damage. So glad that everyone is ok. We will be looking forward to our fish pie and prawn salad when you are up and running again."