Stoltenberg stepped down as secretary general of NATO last month after 10 years at the head of the US-led military alliance.
The Norwegian will take up his new role in the new year, following the conclusion of the MSC's next annual meeting in February.
"Few international platforms are as important as the MSC to promote conflict prevention, dialogue, and international cooperation," Stoltenberg said in a statement.
The son of a politician, Stoltenberg served as Norway's prime minister for a total of 10 years in two stints between 2000 and 2013.
His term as NATO chief was extended four times by the members of the alliance.
As secretary general, Stoltenberg had to execute a careful balancing act as NATO came under different pressures.
The election of Donald Trump in 2016 threatened to tip NATO into crisis, with the president threatening to withdraw vital US military protection from allies that did not spend enough on defence.
Subsequently, NATO has gained in relevance as the threat from Russia has grown, following Moscow's 2022 invasion of Ukraine.
Stoltenberg was replaced as head of NATO by the former Dutch Prime Minister Mark Rutte at the end of last month.
The Norwegian in turn will replace German Christoph Heugsen, otherwise best known as one of former Chancellor Angela Merkel's most senior advisors, as chair of the MSC.
The security conference, hosted every year at the Bayerischer Hof hotel in Munich, is a fixture in the diplomatic calendar.
The meet-up regularly attracts senior figures from across politics and industry, with speakers in recent years including Ukrainian President Volodymyr Zelensky and US Vice president Kamala Harris.
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