The airline also said Wednesday it will lay off 100 corporate and operational support employees, on top of the 4,000 workers it has laid off since March.
The decision will eliminate 100 weekly flights to and from the Atlantic region, or almost 80 per cent of seat capacity.
"It has become increasingly unviable to serve these markets", said WestJet CEO Ed Sims.
The airline says it has worked to keep essential air service going since the start of the pandemic, but demand for travel is being severely limited by restrictive policies.
Alicja Siekierska is a senior reporter at Yahoo Finance Canada. WestJet increased fees it charges domestic travellers in September by 30 per cent, or between $4 and $7 per flight, citing a rate increase imposed by Nav Canada, the federal organization that operates air traffic control operations.
All flights to and from Moncton, Fredericton, Sydney, Charlottetown and Quebec City will be discontinued as of November 2.
Prior to Wednesday's announcement, WestJet was reportedly the only Canadian airline still retaining 100 per cent of its pre-pandemic domestic flight network. Before the pandemic, the route had daily WestJet service.
It's impossible to predict, he added, when the Atlantic routes will return.
Spokesperson Morgan Bell says eight people from each of the affected airports in Moncton, Fredericton and Charlottetown will be released.
More than 70 per cent of the carrier's fleet remains grounded. A WestJet flight from Calgary arrives at Halifax Stanfield International Airport in Enfield, N.S. on Monday, July 6, 2020.