Previously, a charge of US$7 was levied per month for private repositories. There will be a limit of up to three collaborators per repository.
GitHub was purchased by Microsoft for US$7.5 billion in June last year.
In a blog post, GitHub chief Nat Friedman said: "Many developers want to use private repos to apply for a job, work on a side project, or try something out in private before releasing it publicly.
Additionally, the company announced that it had created a unified product known as GitHub Enterprise for Enterprise Cloud (formerly GitHub Business Cloud) and Enterprise Server (formerly GitHub Enterprise).
"Organisations that want the flexibility to use GitHub in a cloud or self-hosted configuration can now access both at one per-seat price," Friedman said.
"And with GitHub Connect, these products can be securely linked, providing a hybrid option so developers can work seamlessly across both environments."
At the time Microsoft announced the acquisition of GitHub, there was a mixed reaction, with open-source developers wary of the Redmond-based software giant's motives.
One security researcher, Mustafa Al-Bassam, raised the possibility that the NSA could now gain access to the code of GitHub as Microsoft has, in the past, allowed the spy agency access to its systems.