A notice on the website of the European Commission, the executive arm of the EU, indicated that Microsoft had asked on 14 September for the acquisition to be approved.
The EC has set a provision deadline of 19 October for either approving or else beginning an investigation if it deems the deal would raise anti-competitive concerns.
Microsoft announced the deal on 5 June at which time GitHub had about 28 million developers working on 80 million repositories.
There has been mixed reaction to the acquisition, with open-source developers wary of the Redmond-based software giant's motives in buying GitHub.
The last big Microsoft acquisition approved by the EU was the purchase of LinkedIn for US$26 billion.