The 30-year-old Melbourne playmaker has edged out fellow Storm teammate Harry Grant and Gold Coast prop and captain Tino Fa'asuamaleaui for the role.
He replaces former skipper Daly Cherry-Evans, who was axed after the 18-6 loss in game one of this year's series.
Munster will take charge for game two in Perth next Wednesday night as the Maroons aim to square the ledger.
The Queensland talisman hit rock bottom when he was caught in a "white powder scandal" at the end of 2021 with former Storm teammate Brandon Smith. He went into rehab and his career was in the balance at that point, but he's turned his career and life around since.
Munster had a tear in his eye when asked if he ever envisaged being Maroons captain.
"It's all pretty emotional. If you asked me that question five or ten years ago everyone would have laughed in your face," Munster said.
"I think I have developed into a big of a leadership role over the last three or four years and grown up a little bit. I know that's hard to say.
"I'm very excited to lead this team out. I know it's terrible circumstances with Chez (Cherry-Evans) I'm really good close mates with him. It's disappointing but someone had to take the role."
At 9.30pm on Monday night coach Billy Slater texted Munster to ask him to come to his hotel room at their Sunshine Coast resort.
"I was thinking what could this be about? I could be getting dropped or maybe I'm 18th man," Munster said.
"Billy just brought me into the room and said 'look mate, I want you to be the captain for Queensland and I think you will do a great job'.
"He pretty much just told me to lead by my actions. I don't need to be a talker or go out there and try motivate the boys. They have enough motivation as it is."
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