The Farney County lost to Donegal after a replay at the semi-final stage of the Ulster SFC and then crashed out to Longford in a shock defeat in the All-Ireland qualifiers second round.
A statement issued by Monaghan GAA on Tuesday confirmed O'Rourke's decision.
O'Rourke indicated he would continue "following a period of reflection".
In his four years in charge to date, Monaghan have won the Football League Division Two and Three League titles, and reached a Division One semi-final in 2015.
They will return to compete in Division One in 2017.
O'Rourke's men have also won two Ulster Championships in 2013 and 2015 and were defeated finalists in 2014.
"Malachy and his backroom team are looking forward to the challenges a new season will bring," the statement indicated.
Malachy O'Rourke has opted to remain as Monaghan manager for a fifth successive season despite a disappointing showing by the county in the Championship.