The Commission said that effective competition in the relevant markets would continue and Microsoft would have no incentive to undermine the open nature of GitHub's platform.
Microsoft in June announced to acquire GitHub, the world's leading software development platform. Github has a community of over 28 million developers worldwide. The acquisition is expected to close by the end of this calendar year.
The Commission said the transaction would raise no competition concerns in any of the affected markets and cleared the case unconditionally.
"Microsoft and GitHub both supply tools that organisations and individuals use when developing and releasing software," said the Commission.
The two companies will empower developers to achieve more at every stage of the development lifecycle, accelerate enterprise use of GitHub, and bring Microsoft's developer tools and services to new audiences.
"Microsoft is a developer-first company, and by joining forces with GitHub we strengthen our commitment to developer freedom, openness and innovation," Satya Nadella, CEO, Microsoft, had said in a statement.
Microsoft Corporate Vice President Nat Friedman, founder of Xamarin and an open source veteran, will assume the role of GitHub CEO.
GitHub's current CEO, Chris Wanstrath, will become a Microsoft technical fellow, reporting to Executive Vice President Scott Guthrie.
Github platform hosts a growing network of developers in nearly every country representing more than 1.5 million companies across healthcare, manufacturing, technology, financial services, retail and more.