Chautauqua is historically significant for it is one of the last remaining companies still in business that once flew as a part of Allegheny Commuter, one of the first regional franchisee systems combining independent regional and commuter airlines under one seemingly contiguous and seamless brand. Ironically, it no longer services the Chautauqua County-Jamestown Airport from which it began.
In 1994, Chautauqua Airlines posted its first loss in 20 years. The loss can be attributed to the crash of American Eagle Flight 4184. Media coverage of the crash spread quickly, and because of its association, Chautauqua Airlines lost passengers who had come to distrust commuter planes. However, Chautauqua Airlines bounced back, while renewing its code-share agreement with US Airways on May 8, 1994. To better support its growing operations, the corporate headquarters were relocated to Indianapolis, Indiana.
Chautauqua was acquired by Wexford Management in January 1998 and was subsequently realigned under a holding company, Republic Airways Holdings.
In 1998, Chautauqua entered into an agreement with Embraer for the purchase of ten 50-seat Embraer ERJ-145 regional jet aircraft. In 1999, Chautauqua entered into a 10-year code-share agreement with Trans World Airlines to operate at least 15 ERJ-145s for the airline. In June 2001, American Airlines, who had purchased TWA, renewed the existing regional jet service with Chautauqua for feeder service at St. Louis using 44-seat ERJ-140 aircraft. In March 2001, Chautauqua entered into a partnership with America West to operate as an America West Express affiliate using 12 ERJ-145 jets in the Eastern United States, but ended this service in February 2003. In November 2002, Chautauqua began flying regional jet service to Florida for Delta Air Lines. In March 2004, United Airlines announced that Chautauqua Airlines would operate 16 50-seat regional jets for United Express.
In 2004, Republic Airways Holdings announced a new jet-service agreement with US Airways for the operation of Embraer E170 and Embraer E190 aircraft. Chautauqua was one of the first U.S. operators of the E170, but was forced to transfer these aircraft to sister company Shuttle America in 2005 after the pilots’ union at American Airlines claimed the aircraft violated a “scope clause” regulating the size of regional aircraft operated under American brands. In the first half of 2007, Chautauqua took delivery of 24 Bombardier CRJs and flew them under a code-share agreement with Continental Airlines. Some of these aircraft were previously owned by Atlantic Coast Airlines (Independence Air), and some were owned by Comair. Chautauqua eventually phased out all of its CRJ aircraft.
In April 2010, the Federal Aviation Administration proposed a US$348,000 fine against Chautauqua Airlines for allegedly not performing required inspections for three years. The FAA alleged that the airline flew an Embraer 145 jet for 43 days past the time one of its inertial navigation units should have been replaced.
In October 2012, Republic Airways Holdings reworked a deal with partner Delta Air Lines, part of the company's broader effort to trim costs and boost revenue amid a decline in demand for regional airline service, to operate seven additional 50-seat Embraer 145 planes under the Delta Connection brand.
In the spring of 2014, Republic Airways Holdings announced that it would begin to pull down much of Chautauqua's flying. Specifically, it would not renew it's contract with United Airlines to fly ERJ-145s out of Cleveland and that it would ground all 14 ERJ-145s on April 1 in response to a shortage of qualified pilots. This was shortly followed by an announcement that it would also not seek renewal of its AmericanConnection contract. Chautauqua's operation as AmericanConnection ended on August 18, 2014.
On July 28, 2014, Republic Airways Holdings announced that Chautauqua Airlines will be absorbed into Shuttle America "by year-end" to reduce costs. Chautauqua's only remaining aircraft, 41 ERJ-145s, will be transferred to the Shuttle America operating certificate, effectively abandoning Chautauqua's operating certificate.