Republic Airlines

In 1999, Republic Airways Holdings incorporated a new subsidiary, "Republic Airline, Inc." but the subsidiary had no activity prior to 2004 and no ability to operate aircraft prior to 2005. In 2004 the holding company activated Republic Airways in reaction to a pilots' suit against American Airlines.

American had awarded the flying of 44-seat regional jets to Chautauqua Airlines, then the main operating subsidiary of Republic Airways Holdings. However, Chautauqua later started to operate 70-seat regional jets on behalf of United Airlines, and this caused American to be in violation of its pilot union scope clause, which prevented an airline from operating on behalf of American if that airline was operating jet aircraft of more than 50 seats, even if such aircraft were operating on behalf of a carrier other than American. To repair the situation, Republic Airways Holdings activated Republic Airline, and upon Part 121 certification in 2005 allowing Republic Airline to operate commercial service. Republic Airways Holdings then transferred the offending 70-seat regional jets from Chautauqua to Republic Airline. American was then no longer in violation of its pilot union scope clause. Republic Airways Holdings paid $6.6 million to the pilot union of American Airlines to settle the issue.

US Airways' pilots had a scope clause prohibiting the airline from operating large regional jets such as the Embraer 170. The airline negotiated around this clause by offering flight deck jobs to laid-off US Airways pilots, in a program known as "Jets for Jobs". This agreement created a subsidiary, MidAtlantic Airways. As part of US Airways' bankruptcy restructuring, the 25 Embraer 170s delivered to MidAtlantic were bought by Republic to help US Airways come out of bankruptcy; Republic operates them along with additional newly delivered aircraft.

In 2007, Frontier Airlines signed an 11-year service agreement with Republic Airways. Under the agreement, Republic would operate 17 Embraer 170 aircraft for Frontier. The first aircraft was placed into service in March 2007, and the last aircraft was expected to be placed into service by December 2008. On April 23, 2008, Republic Airways Holdings (parent of Republic Airline) terminated its service agreement with Frontier Airlines, which entered Chapter 11 bankruptcy in early April 2008. Subsequently, Republic Air Holdings purchased Frontier Airlines in bankruptcy. Frontier-branded Republic Airways E190 aircraft provided regional capacity support. In September 2013, Republic Airways Holdings sold Frontier Airlines. As part of the sale, Republic Airways negotiated a provision that prevented the Frontier-branded E190s from being flown.

On February 1, 2008, Republic Airways opened a base at John Glenn Columbus International Airport in Columbus, Ohio.

On September 3, 2008, Republic signed a new 10-year codeshare agreement with Midwest Airlines. The aircraft would be based at Kansas City International Airport beginning October 1, 2008. Twelve aircraft would be placed in service with Midwest. On June 23, 2009, Republic announced it would acquire Midwest Airlines for $31 million.

In January 2013, Republic Airways Holdings reached a capacity purchase agreement with American Airlines to operate Embraer 175 airplanes under the American Eagle brand beginning in mid-2013. Republic began service as an American Eagle affiliate on August 1, 2013, from Chicago to New Orleans, Pittsburgh, and Albuquerque.

On February 25, 2016, the airline filed for Chapter 11 bankruptcy protection. The airline was hit hard because of pilot shortages, but a new contract ratified in October 2015 helped restructure the airline. At the time of filing, Republic Holdings claimed $2.97 billion in liabilities and $3.56 billion in assets. On November 16, 2016, Republic Airways Holdings filed their reorganization plan, with the intention to emerge from Chapter 11 during the first quarter of 2017.

It was announced that parent company Republic Airways Holdings would merge subsidiaries Shuttle America and Republic Airways into one company, with Republic Airways being chosen as the surviving company. On January 31, 2017, Shuttle America merged with Republic Airways. In December 2018, the operating division was renamed Republic Airways to match its parent company.

On September 21, 2021, Republic Airways announced it will move its corporate headquarters to Carmel, Indiana. The headquarters, training facility and hotel was a $200 million project which opened on February 9, 2026.

As of November 25, 2025, Republic Airways has the largest fleet of Embraer 170 and Embraer 175 aircraft in the world.

Merger with Mesa Airlines

On April 7, 2025, Republic Airways Holdings announced that it would acquire Mesa Airlines in an all-stock merger. Under the terms of the agreement, Republic shareholders will own approximately 88% of the merged company, while Mesa shareholders will retain between 6% and 12%.