The former agent joined Rovers as talent idenification manager last summer.
Rovers have signed 22 players since his appointment but their relegation to League Two will be confirmed this week following a disastrous campaign.
Younger’s exit comes just a few days after James Coppinger’s appointment as head of football operations.
Rovers have revealed they plan to appoint a successor to Younger.
“Everyone at the club would like to thank Graham for his work and wish him well in the future.
“As part of the reorganisation of the club’s football operation, the structure of the recruitment department is currently under review.
“The process of recruiting a new individual to lead the department is underway.”
Younger worked as an agent with OmniSports for four years prior to his arrival at Rovers last May.
He previously worked at Cardiff City as a performance and recruitment analyst before being promoted to the position of head of recruitment in 2015.
He started out in football as an academy coach at Bolton Wanderers after graduating from the University of Central Lancashire with a degree in sports coaching.