The stores at 1601 W. 41st St. and 4501 E. Arrowhead Parkway are scheduled to close by April 15.
The company says, "Today's announcement provides clarity about the path forward for us, and we are confident the outcome will be a stronger Shopko".
The company has formally filed for Chapter 11 bankruptcy protection, officials announced Wednesday.
In a news release, the Shopko said, "The Company is seeking to facilitate the restruing as a result of excess debt and ongoing competitive pressures".
As part of the reorganization, Shopko plans to close an additional 38 stores (on top of some 45 during the past year), relocate more than 20 Optical centers to freestanding locations and conduct an auction process for its pharmacy business.
For the stores that remain open, it will be business as usual, the company said.More news: UK PM May holds Brexit talks; opposition dubs them a ‘stunt’
More news: 'Super blood wolf moon' eclipse to darken skies
More news: Burger King mocks Trump on Twitter over his misspelling of 'hamburgers'
The company's assets are listed by court documents at between $500 million and $1 billion, with liabilities estimated between $1 billion and $10 billion.
"This decision is a hard, but necessary one", Shopko CEO Russ Steinhorst, said in a news release. The petitions have been filed in the U.S. Bankruptcy Court for the District of Nebraska.During the restructuring process, Shopko will continue to operate and serve its customers, vendors, partners and employees.
Shopko has obtained $480-million in debtor-in-possession financing from certain prepetition secured lenders led by Wells Fargo, N.A.to fund operations during the bankruptcy process. "Except for those stores that we are closing, we are continuing to honor return policies, warranties, gift cards and merchandise credits, as well as our loyalty programs", the news release said.
The complaint says Shopko made misrepresentations "regarding its solvency" and ability to pay for products it purchased from McKesson.
An article in the Ely Echo said that Shopko had not made its monthly lease payment to the property owner in Ely, where there is a store. The Powell hospital is accepting bids on the $577,463 project through January 24.
Founded in 1962 and headquartered near Green Bay, Wisconsin, Shopko Stores Operating Co.