Thomson, who last October was appointed as football operations manager, was given the promotion tick for the key role at the Broncos' board meeting on Tuesday.
Last year the Broncos went to market for an overarching general manager of football after Thomson had joined the club.
The Broncos used a recruitment agency to search far and wide for the right fit but came back to a candidate who was already in the building.
They were initially seeking an omnipresent figure who could give new coach Michael Maguire elite support, in much the same way as Frank Ponissi does for Melbourne mentor Craig Bellamy.
The size of the Brisbane operation has led to roles being shared.
Founding NRLW head coach Paul Dyer will lead the NRLW program, Thomson will helm the NRL operation, while Simon Scanlan has oversight of recruitment and retention.
Such has been Thomson's positive influence and smarts since his arrival that it was decided to elevate him to the new high tensile task.
Thomson knows how clubland works, but also how the NRL operates.
He was most recently employed by the NRL as the elite performance manager for the Kangaroos and has a long association with Maguire.
He linked with South Sydney in 2012, when he was the high performance manager and an integral mover and shaker behind the club's 2014 title win.
He was responsible for overseeing training, medical staff and practices of the club.
Prior to that he was head trainer at the Storm during a dream run for the NRL powerhouse, while he was also high performance manager of the Melbourne Rebels in their inaugural Super Rugby season.
Last October, club chief executive Dave Donaghy highlighted the importance of finding the right person for the role of football general manager.
Donaghy spoke of the investment the club was making to drive cultural and performance improvements after finishing 12th last year, standards Thomson will now enhance in partnership with Maguire.
He also gave a telling insight at the time about why a single person could not oversee all the Broncos' on-field operations.
"You're talking about NRL, NRLW and we've got two academy programs and three affiliate clubs," Donaghy said.
"We want to have really strong relationships with both NRL game development, the Queensland Rugby League and our game development programs.
"Just given the focus and scrutiny on the NRL program, we felt it was too much to have one person really attached to that when we've got such a wide, vast football program.
"That's not including our salary caps across both teams and football department caps. It's a big, core part of our business and we make no apologies for wanting to invest in it."
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