"I've been harassed by 'leadership' at GitHub for two years and I am the first developer to quit," Julie Ann Horvath wrote on Twitter last Friday.
In response, chief executive Chris Wanstrath said a co-founder and an engineer were put on leave.
"We have begun a full investigation," he wrote in a blog post.
GitHub, founded in 2008, is a web-based hosting service for software developing projects.
It has grown rapidly in recent years, fuelled by its social networking platform which allows users to share code and trade tips.
As of April 2013, the company said it had over 3.5 million users.'Done differently'
In a series of tweets on Friday, Ms Horvath detailed what she said was "character assassination" and "aggressive behaviour" from a GitHub co-founder and engineer.
"I had to permanently alter my career path and risk personal safety and further harassment for there to be action taken," she wrote, saying the company ignored her complaints
"Nothing will be resolved on my end until both of those men are asked to step down."
In his blog post, Mr Wanstrath said he "would like to personally apologize to Julie".
Mr Wanstrath also noted that while GitHub has grown quickly over the past few years, it only hired a human relations manager in January.
"It's certain that there were things we could have done differently," he wrote.