In a statement, the company said, "There was mutual agreement that it was time for new leadership to address the challenges that face the company."
Board member G. Mike Mikan was named interim CEO and will lead the search for a new chief executive, Best Buy said.
"We thank Brian Dunn for his many years of service to the company and wish him well in his next endeavors," company founder Richard Schulze said. "As we move forward, we are very pleased to have a strong leader with Mike Mikan's credentials as interim CEO."
Dunn said he had "enjoyed every one of my 28 years with this company," adding he expected the firm to have "a strong future."
"There were no disagreements between Mr. Dunn and the company on any matter relating to operations, financial controls, policies or procedures," the statement said.
The shift, however, comes just two weeks after Best Buy said same store sales declined 1.7 percent in its latest fiscal year, only slightly better than the 1.8 percent decline from the previous year.
In late March, the company announced a restructuring plan that would trim $800 million from its operating expenses with the closure of 50 big box stores and savings of $300 million in corporate support and structure, $300 million in retail operations and $200 in goods on the shelf.