Whiffin joined the club in 2005 as analyst, progressing to the roles of head of analysis and assistant coach.
The Exiles are yet to confirm their coaching set-up for next season having been relegated to the Championship.
A rugby department review began last month, which included head coach Tom Coventry and assistant coaches Clark Laidlaw and Grant Doorey.
London Irish have parted company with assistant coach Richard Whiffin following Premiership relegation.