In 2008, Pilot bought out Marathon's interest in the business and formed a partnership with CVC Capital Partners, an international private equity firm.

Flying J's oil and refining operations as well as its banking and insurance division remained separate from the new company,[14] and was subsequently renamed FJ Management Inc.[15] To settle antitrust concerns with the Federal Trade Commission, Pilot sold 20 Pilot Travel Centers locations and six Flying J locations to Love's Travel Stops & Country Stores on June 30, 2010.

[19] On October 3, 2017, it was announced that Warren Buffett-controlled Berkshire Hathaway would acquire 38.6% of Pilot Flying J, with plans to increase its stake to 80% in 2023.

Pilot Flying J's main restaurants include Arby's, Chester's Chicken, Dairy Queen, Denny's, Hardee's, McDonald's, Pizza Hut, Subway, Taco Bell, Wendy's, and Cinnabon.

Recently they have also added Huddle House (full-service restaurants), Moe's Southwest Grill, and Dunkin Donuts.

[22] In 2013, the company sponsored Annett in the Richard Petty Motorsports number 43 Ford Mustang in NASCAR's Nationwide Series.

Before the deal, Bosselman bought diesel fuel from Pilot and continues to do so for its remaining travel center location in Grand Island, Nebraska.

[28] On April 15, 2013, the headquarters of Pilot Flying J, located in Knoxville, Tennessee, was raided by FBI and IRS agents as part of an "ongoing investigation".

On April 16, CEO Jimmy Haslam reported the investigation involved claims of failure to pay rebates to trucking customers.

[32] On Tuesday, July 16, 2013, a federal judge in Arkansas granted preliminary approval to a proposed settlement agreement between Pilot Flying J and several trucking companies that had sued over allegations of fuel rebate fraud.

[33] Pilot Flying J paid restitution to customers and agreed to pay a $92 million penalty pursuant to a Criminal Enforcement Agreement.