A Biman Bangladesh Airlines aircraft departed for Manchester on Thursday afternoon, while domestic flights have been operating since the morning, according to the airport's Manager Hafiz Ahmed.
As floodwaters engulfed the runway, the authorities on Jun 17 suspended all flight operations before closing the airport for three days.
The water began to recede on Sunday and the runway was almost entirely clear a day later.
However, it was not possible to operate flights at the airport sooner as the approach lights remained submerged on Wednesday, according to Hafiz.
Several planes operate in the airport daily and travel mostly from Sylhet to and from Dhaka and London.