Flint Hills, owned by multinational corporation Koch Industries Inc., said it would shut down the refinery no later than June 1, halting the production of jet fuel and other refined petroleum products.
The company said it would continue selling fuel from its Anchorage and Fairbanks terminals, though petroleum supplies would come from other sources.
Flint Hills said it made the decision to close the refinery because of the high costs of cleanup that resulted from contamination at the North Pole site from its previous owner, Williams Cos. Inc.
"With the already extremely difficult refining market conditions, the added burden of excessive costs and uncertainties over future cleanup responsibilities make continued refining operations impossible," Mike Brose, refinery manager for Flint Hills, said in a statement Tuesday.
Alaska Gov. Sean Parnell said in a statement he was "extremely concerned" by the loss of jobs from the closure of the refinery, which employed more than 100 people.
Parnell last month expressed disappointment when Shell said it wasn't planning on drilling off the coast of Alaska this year, citing complications from a legal challenge from environmental campaigners.
Once a national leader, Alaskan oil production has experienced a steady decline.