Graphene started in 2011 as a research project at Stony Brook University, led by Chia-Che Tsai and Don Porter, contributed by many students and first released in 2014. In 2015, SGX support was developed in cooperation with Intel Labs, along with the first Graphene release for SGX. Over the subsequent years, multiple research and industrial users have contributed to the project. In 2017, Golem, Invisible Things Labs (ITL), and Intel began making significant investments in the project.

In 2018, the project adopted a formal working group and project policies, in order to encourage and manage growth of the community. The working group is guiding the process of making Graphene production-ready, and setting a roadmap for future development. The group is lead by a team from Golem and ITL; Intel; and the original researchers (now at UNC Chapel Hill and Texas A&M University).