The announcement is a massive boost to the club as the Cowboys prepare to host their Telstra Premiership season launch in Townsville on Friday ahead of star half Johnathan Thurston's final season.
The Townsville-born 26-year-old will line up next to Thurston this year before taking over as the chief playmaker in 2019.
Morgan had previously said he did not want to leave the club that signed him as a teenager and he has proved good to his word.
"I'm stoked to be staying at the Cowboys, a club I grew up supporting and, later in life, proudly playing for," Morgan said.
"Townsville is my home, I've been involved with the Cowboys since I was 17, I made my NRL debut as a Cowboy and all the positives in my career have come from me proudly wearing this great team's colours.
"To be able to continue that journey and keep playing alongside a great bunch of blokes – and for our excellent coaching staff and our wonderful, passionate fans and members – is pretty special."
To have him remain a Cowboy for a further five seasons is tremendous news for Michael, the club and all of North Queensland.
Cowboys general manager of football Peter Parr told NRL.com earlier how the club knew they had someone within their own ranks to fill the void when Thurston left.
While Parr insisted no-one would ever replace the irreplaceable Thurston, he acknowledged that by the time he'd retired Morgan would have played 140 to 150 NRL games, featured in several finals series and have learned plenty playing alongside the champion halfback.
Throw in his State of Origin and Australia experiences alongside Thurston and Cronk and the Cowboys were of the belief that Morgan had done as good an apprenticeship as anyone possibly could
His stellar performances as the chief playmaker last year following Thurston's season ending shoulder injury confirmed to Cowboys' powerbrokers that he was the man to take control of the club into the future.
"Michael was a Townsville junior, was identified at an early age, and came up through our elite pathways system, from which point he earned an NRL contract with the club," Parr said after securing Morgan's signature.
"It's no secret the sort of career that Michael has had since then.
"Since making his NRL debut as a teenager in 2010, he has helped the club to its maiden premiership and two grand final appearances in three seasons. He's also made his Queensland and Australian debuts while playing for the Cowboys, something he and the club can be extremely proud of.
"To have him remain a Cowboy for a further five seasons is tremendous news for Michael, the club and all of North Queensland."
Former Cowboys board member Ben Ikin told NRL.com recently that replacing Johnathan Thurston, one of the greatest players the game has seen didn't mean the Cowboys needed "like for like".
"It just has to be a player that can have as big an influence on the result as JT did," he said.
"I think Michael Morgan has shown himself, particularly last year, to have that ability."
Morgan is a North Queensland product who was born in Townsville, attended Ignatius Park College and played his junior football for Townsville Brothers.
Since rising through the under 20s ranks he has played in 128 NRL games and won the 2015 premiership.
He has also played in eight State of Origin games for Queensland in three series wins. Morgan was a key member of Australia's World Cup winning side last year and has played 12 Tests in the green and gold.