His appointment comes as speculation grows that Glencore will privatise its thermal coal business, with Glasenberg touted as a possible buyer of the business.
Nagle would then be allowed to manage the rest of Glencore's operations adhering to the required environment and social governance rules expected of public companies.
Glencore chairman Tony Hayward said the company was committed to adapting to a low-carbon economy.
"As Ivan hands over to Gary, he does so at a time of huge change," he said.
"As the world moves to recover from the impacts of the COVID-19 pandemic, while also addressing the challenge of climate change, our industry has a significant opportunity to contribute to the economic recovery by providing commodities essential to the transition to a low-carbon economy."
Glasenberg said Glencore was one of the world's largest diversified miners and marketers of commodities.
"Today, our diversified portfolio uniquely positions us to play an essential role in the global transition to a low-carbon economy," he said.
"I have worked with Gary since he joined the company 20 years ago. I have always regarded it as a critical part of my job to develop the next generation of leadership at Glencore and I am proud of the strong leadership team that we developed from which we were able to select Gary."
Nagle said the company would continue to operate safely and responsibly.
He joined Glencore in 2000 in Switzerland as part of its coal business development team.
Nagle was heavily involved in seeding a portfolio of assets to Xstrata in 2002, in conjunction with its initial listing on the London Stock Exchange.
He then worked for five years from 2008 to 2013 in Colombia as CEO of Prodeco, Glencore's Colombian coal operation before moving to South Africa to take on the role of Head of Glencore's Alloys Assets between 2013 and 2018.
Nagle also served on the board of Lonmin from 2013-2015and represented Glencore on the Minerals Councils of Australia and in Colombia.