He most recently served as the head coach of Bangladesh Premier League club Muktijoddha Sangsad KC.
Raja Isa started coaching for Selangor FA youth teams but was brought to Indonesia as part of Irfan Bakti's coaching staff at Persipura Jayapura in 2007.
He guided Persipura to the 2007 Copa Indonesia Final, where his team was beaten 3-0 on penalties by Sriwijaya FC after 1-1 in normal regulation time.
In 2008, after he was released by Persipura, Raja Isa was appointed as the head coach of PSM Makassar.
This biographical article related to Malaysian association football is a stub.