During the late 1980s, the Kalitta brand name continued to appear on many of the company's cargo aircraft. In 1990 and 1991, AIA flew 600 missions in support of Desert Shield/Desert Storm.
In 1997, AIA merged with Kitty Hawk Inc. and Conrad Kalitta resigned to start Kalitta Leasing for buying, selling and leasing large aircraft. In April 2000 Kitty Hawk International (the former AIA) ceased operations. Kalitta decided to rescue it and the new airline, Kalitta Air, began operations in November 2000, using the operating certificate and assets of the former airline.
On April 21, 2017 Kalitta Air retired its final Boeing 747-200F from service. This was one of the relatively few then remaining in service.
On August 18, 1993, American International Airways Flight 808, a Douglas DC-8-61 (N814CK) with three crew members on board struck level terrain 1,400 feet west of the approach end of the runway while landing at Guantanamo Bay, Cuba. The aircraft approached from the south and was making a right turn for runway 10 with an increasing angle of bank in order to align with the runway. At 200-300 feet AGL the wings started to rock towards wings level and the nose pitched up. The right wing appeared to stall, the aircraft rolled to 90-degree angle of bank and the nose pitched down. All 3 crew members survived with serious injuries, though the aircraft was completely destroyed by the impact and post-crash fire. Probable cause of the accident attributed primarily to the impaired judgment, decision-making, and flying abilities of the captain and flight crew due to the effects of fatigue resulting from extended flight/duty hours. This accident was also featured in the 2019 Season 19 of Mayday/Air Crash Investigation Episode Titled "Borderline Tactics".
On October 20, 2004, a Kalitta Air Boeing 747 (N709CK), with five crew members on board, experienced mechanical difficulties with one of the four engines and diverted to land safely at Detroit Metropolitan Airport. No one was injured. It was discovered after landing that the number 1 engine had separated from the airplane as it climbed through 16,000 feet over Lake Michigan. The engine was later recovered for inspection.
On May 25, 2008, a Boeing 747-209F/SCD (N704CK serial number 22299/462) from the company's fleet overran runway 20 at Brussels Airport. The aircraft broke in three and came to a complete stop in a field bordering the runway. There were four crew members and one passenger on board, and no injuries were reported. The aircraft destined for Bahrain International Airport was loaded with 76 tons of goods, half of which was diplomatic mail. Belgian investigators announced that the accident was caused by the decision to Reject the Take-Off 12 knots after passing V1 speed. The Air Accident Investigation Unit (AAIU) of the Federal Public Service Mobility and Transport had investigated the accident.
On July 7, 2008, a Boeing 747-209B (N714CK serial number 22446/519), crashed shortly after departing from El Dorado International Airport in Bogotá at 3:55 a.m. The aircraft was en route to Miami, Florida, with a shipment of flowers. After reporting a fire in the number 4 engine, the crew attempted the return to the airport. However, after engine number 1 failed as well, the aircraft could not maintain altitude and crashed near the village of Madrid, Colombia. The aircraft's empennage hit a ranch house, killing a 50-year-old man and his 13-year-old son who lived there (a report of this crash on Airdisaster.com indicated a third fatality on the ground). The flight deck separated from the remainder of the aircraft, and the crew of eight survived with light to serious injuries while the rest of the airframe was consumed by fire.
On July 26, 2008, a Learjet 35, operating as Flight 66 declared an emergency, and it was later found that the pilot/crewmember whose transmissions got gradually slower, was suffering from hypoxia. He descended through 11,000 feet, and made a safe landing.
For the 1997 film Air Force One, the producers rented one of Kalitta's Boeing 747-212B aircraft N703CK and repainted it to replicate the iconic Air Force One livery.
The TV program MythBusters featured one of Kalitta's Boeing 747s (tail number N700CK) in Episode 90: "Supersized Myths", that originally aired on November 14, 2007. In this myth the build team revisited the myth of "Jet Taxi", the story of a taxi that got stuck behind a jet taking off resulting in the taxi flipping over due to the jet blast. This myth was found to be confirmed, in that a jet could flip a taxi as well as a school bus and a light aircraft. MythBusters featured another Kalitta Air 747 (tail number N709CK) in the episode "Storm Chasing Myths" that originally aired on October 13, 2010.