It began scheduled service under contract with IBM in 1970 between Manassas, Virginia, near Washington, D.C., and Dutchess County Airport near Poughkeepsie, New York.

After Presidential went defunct, Colgan and his son, Michael J., restarted service under the name National Capital on a Washington-Dulles to Binghamton, NY, route on December 1, 1991.

However, in 2005 Colgan acquired additional Saab 340 aircraft and resumed service as Continental Connection out of Houston.

Early on the morning of September 11, 2001, the day of the September 11 attacks, al-Qaeda hijackers Mohammed Atta and Abdulaziz al-Omari flew on Colgan Air Flight 5930 from Portland International Jetport in Portland, Maine to Boston Logan Airport in Boston, where they boarded American Airlines Flight 11.

Initially serving Charleston, West Virginia, and Westchester County Airport in White Plains, New York, Colgan expanded its United Express service to include State College, Pennsylvania; Charlottesville, Virginia; Allentown, Pennsylvania; and Binghamton, New York.

Under the terms of the purchase, Colgan's regional aircraft fleet continued to operate independently of Pinnacle Airlines Corporation's major subsidiary, Pinnacle Airlines, whose all regional jet fleet continued to fly and operate in the livery of Northwest Airlink.

[2] Colgan Air began providing service out of Newark Liberty International Airport (as Continental Connection) starting in early 2008.

Colgan had previously operated as Continental Connection from IAH with Saab 340 aircraft prior to Continental-United merger.

The headquarters of Colgan Air were, at the end of the airline's life, located in Memphis, Tennessee.

[6] In October 2009, Pinnacle Airlines Corp. tried to get additional incentives from the State of Tennessee as the Colgan headquarters were about to move.

[8] Helaine Becker, a transportation analyst employed by Jesup & Lamont Securities Corp, believes that the moving of Colgan will help reduce costs; she said that the company did not need two corporate headquarters and that "I think it has more to do with that than anything else.