After returning home in 1991, he was appointed an associate chair in the Department of Aeronautical Engineering at Istanbul Technical University.

Between 2002-03, he worked as the head of the Research, Planning and Coordination Department at Advance Innovative Technologies Inc. in New York.

In 2003, he returned to Turkey and was employed by Turkish Airlines in Istanbul becoming its executive vice president in charge of technical affairs.

In April 2005, Kotil was appointed to assume the position of the General Manager and CEO of the biggest airline company of Turkey.

Kotil retired as CEO of Turkish Airlines in October 2016, being succeeded by Bilal Ekşi.