The "Heartland Flyer" was started on June 15, 1999, as a joint venture between Amtrak and the Oklahoma Department of Transportation - ending a 20-year absence of passenger train service from Oklahoma and North Texas.

On May 18, 1999, Amtrak started taking reservations for the "NEW" rail service between Oklahoma City and Fort Worth under the provisional name "The New Train." Oklahoma Senator Don Nickles conducted a contest asking Oklahoma children to name the state’s new passenger train. The "Name the Train" program was located on Nickles' web site and provided some suggestions used by Amtrak when picking a train name. During the contest, over 300 children submitted 500 different suggestions. The winning name, "Heartland Flyer," was submitted by 11-year-old Katie Moore.

On June 14th, the 11 car Inaugural Heartland Flyer headed North out of Fort Worth, with dignitaries, including Sen. Nickles, Gov. Frank Keating of Oklahoma, Amtrak officials, and mayors from each of the towns served by the Flyer. Thousands turned out to greet the new train with waves, smiles, banners, and even marching bands.

After the first week of service, Amtrak stated that the Heartland Flyer had carried 1,800 passengers on its route. Riders continued to flock to the Heartland Flyer, and after one month of service, the Flyer carried almost 11,000 passengers.

On June 14, 2000, the Heartland Flyer celebrated its first anniversary. The week started off with an Amtrak static equipment display over the weekend, offering visitors tours of a Superliner Lounge car, a diner, and coach. Family Day activities on Sunday gave visitors hot dogs and soft drinks. In addition, the U.S. Postal Service's "Celebrate The Century" postal train was in Oklahoma City to celebrate the 1 year mark. The Heartland Flyer departed Oklahoma City that morning, with the normal consist plus a Superliner Lounge for VIP's. The train was met in Ardmore with a large crowd and a barbecue lunch. At that point the Heartland Flyer had carried 71,400 passengers in its first year of service - more than three times what Amtrak had stated as being a success.

In October, Amtrak and the Oklahoma Department of Transportation add an additional coach to accommodate fans attending the "Red River Shootout" football game in Dallas between the University of Oklahoma and the University of Texas. Special arrangements are made to provide shuttle bus service between Fort Worth and Dallas. The buses meet the train upon its arrival in Fort Worth and deliver the passengers to their hotels in downtown Dallas and the Market Center Area. The buses then pick up the passengers at the hotels and take them to the train station in Fort Worth for the return trip. This popular excursion often sells out quickly.