In December 2005, the company was acquired by an affiliate of Sun Capital Partners and reverted to private ownership.

In 1999, Shopko purchased Pamida, a regional discount chain that operated mainly in smaller communities of 3,000 to 8,000 people.

In March 1961, Chicago pharmacist James Ruben and other investors announced the formation of a corporation to open a $1 million (equivalent to $7,808,000 in 2023) department store in Green Bay, Wisconsin, to be called "Shopco".

[6] In June 1970, Ruben announced plans for corporate headquarters on Ashland Avenue in Ashwaubenon, Wisconsin.

This was in response to Copps refocusing their efforts on their supermarket business and to make it less of a prime target for shoplifting.

In 1988, a new corporate headquarters opened in Ashwaubenon by the Bay Park Square Mall.The company hit $1 billion (equivalent to $2,223,000,000 in 2023) in sales on the strength of 87 stores in 1988.

[16] In late 1991, ShopKo introduced a "Vision 2000" prototype model, which opened in Sheboygan, Wisconsin, Duluth, Minnesota, Dixon, Illinois, Loveland, Colorado, Longmont, Colorado, and Lacey, Washington, and relocated stores in Marshall, Minnesota, and Mitchell, South Dakota.

Later that year, the firm announced that it would sell ProVantage to Merck & Co. for about $222 million.In May 2000, ShopKo agreed to buy P.M. Place Stores, a 49-location chain, for $22 million (equivalent to $37,000,000 in 2023), with plans to convert those locations to Pamidas.

[28][29] Early in 2001, ShopKo announced the closings of 23 stores and a distribution center, cutting 2,500 jobs and bowing out of Missouri, Indiana, Kansas, and Kentucky.

[39] During the late 2000s, ShopKo started to anchor more shopping centers, such as the ones in Suamico, Wisconsin and North Branch, Minnesota.

[50] Late in 2016, Shopko closed four stores due to poor sales[51][52][53] but also opened one in Ely, Nevada.

[58] Shopko began closing its pharmacies in December 2018 and selling its patient records to local competitors including Walgreens, CVS, Hy-Vee and Kroger.

On January 8, 2019, McKesson Corporation filed a suit against Shopko, seeking $67 million (equivalent to $78,760,000 in 2023) in delinquent payments.

On February 7, 2019, Shopko confirmed the closure of 251 stores or 70 percent of its locations closing in phases between March 2, 2019 and May 12, 2019.

Shopko will exit the states of California, Colorado, Indiana, Kansas, Kentucky, Nevada, New Mexico, Ohio, Oklahoma, Oregon, Texas, Utah, and Washington.

On March 18, 2019, Shopko announced the closure of all remaining stores, after being unable to find a buyer for the chain.

On April 22, 2019, Shopko announced to employees that despite the fact that the company signed a contract for severance pay, only certain states would actually be paid.

In April 2019, Monarch Alternative Capital LP purchased Shopko's optical operations for $8.5 million (equivalent to $9,992,000 in 2023).

[66] By the time it went ceased operations, the company operated 363 stores in 24 states including, but not limited to, California, Iowa, Idaho, Illinois, Indiana, Kansas, Kentucky, Michigan, Minnesota, Missouri, Montana, Nebraska, Nevada, North Dakota, Ohio, Oregon, South Dakota, Utah, Washington, Wisconsin, and Wyoming.

Shopko, with partnerships from Green Bay, Wisconsin-based Bellin Health and other local hospitals, also operated walk-in clinics inside its stores called FastCare.

Shopko Express carried a limited selection of general merchandise, groceries, beer, wine, health and beauty supplies, and over-the-counter medicines.

Shopko sold an assortment of private-label store-brand products, primarily in apparel and general merchandise.

[70] Popular brands included Shopko, Willow Bay, Bailey's Point, NorthCrest, Energy Zone, Soft Sensations, Peanut & Ollie and Green Soda.

[72] Shopko's distribution centers were located in De Pere, Wisconsin, Omaha, Nebraska, Quincy, Illinois and Boise, Idaho.