Control of the business empire passed to New York-born Stenbeck and her siblings after the death of their father, Jan Stenbeck, in 2002. She has chaired the firm since 2007.
"It has been an extraordinary journey of intense work and significant successes. Kinnevik is today stronger than ever, with a great set of assets both in mobile and digital services and the strongest balance sheet in its history," she said in a statement on Friday morning.
Stenbeck will remain heavily involved in the company, but said she is handing over the gavel to South African Tom Boardman, who has been nominated as the new chairman of the board.
"I will continue to support the Kinnevik team as it delivers on all its long-term commitments to its shareholders and investee companies as a non-executive director of the board. As a lead shareholder representative and active owner, I also intend to continue to lead the nomination committee work," she said.
One of the largest listed investment companies in Europe, Kinnevik has shares in firms ranging from startup incubators such as Rocket Internet to media giants such as MTG and Millicom.
Stenbeck has been voted among the most powerful women in the world by Fortune magazine. She is one of the top business women in a country where three quarters of all board members are men, despite its reputation as a leading nation for gender equality, and many expressed surprise at her announcement on Friday.
Christina Stenbeck is stepping down as chairman for Kinnevik and Millicom. Surprised https://t.co/U33uec801X- David Johansson (@ErnstDavidJ) March 11, 2016
Speaking to the TT newswire, Stenbeck said she wanted more time to focus on future business models.
"I started this journey when I was 24, and even if it's hard to believe, I'm almost 39. I have seen myself as an entrepreneur and am returning now to the role I've always wanted."
Her successor Boardman joined the company board as a director in 2011. He has previously held various managerial positions within the South African mining, retailing and banking industries.
"The nomination committee is pleased to nominate Tom Boardman as new chairman of the board. Tom has been an active member of the board for the last five years, contributing with his experience from leading and building companies across multiple industries including telecommunications, financial services, and retail," said Stenbeck.