"Rao will be leaving Skoda Auto at his own request on June 30, 2017," Skoda Auto India spokesperson said in a statement.
The company would be announcing its successor in due course, it added without sharing a timeline.
Rao (57) had joined Skoda Auto India as Chairman and Managing Director on March 1, 2012. Before joining Skoda, Rao ran an international car brand's India activities as Chief Operating Officer.
He had joined the company at a time when it was facing challenges in Indian market specially with customer complaints over sales service.