The Pittsburgh Freethought Community's roots go back a number of years, with its direct lineage going back to the Center For Inquiry – Pittsburgh (CFI), begun in 2004. Some of its indirect roots go back even farther than that, to the American Humanist Association (AHA) chapter called the Humanist Community of Pittsburgh.

Center For Inquiry – Pittsburgh was organized by Professor David Campbell beginning with an appeal to all atheists, agnostics, freethinkers, secular humanists, and similar-minded people to meet together at the Palace Inn ballroom in Monroeville in April, 2004. Those interested in forming a formal group were invited to form a steering committee meeting at Campbell's home. After a few meetings and some discussion of the pros and cons of affiliating with various national groups based in part on their focus and missions, the decision was made to become the CFI Community – Pittsburgh. This was because out of all of the national organizations, CFI had the widest focus and the broadest range of appeal to the nontheistic community, from scientific skepticism, to philosophical exploration of humanism, to social justice issues, and human rights. This became the largest and most active secular group in the Southwestern Pennsylvania area and remained so until it morphed into the Pittsburgh Freethought Community (PFC) in 2017.

During this time, the Humanist group gradually became somewhat moribund with only a couple of active members. Also during this time, a couple of “meetup” groups formed, including Steel City Skeptics which came about in 2008 whose primary function was as a vehicle to sponsor Drinking and Brunching Skeptically. To all appearances, the secular and non-theistic community seemed to be fragmented, although in actuality, most of the leadership of the various groups overlapped, as did many of the functions, and so the scene was thoroughly confusing to newcomers, both local and transplanted.

In 2016, talks began about the necessity of simplifying the secular landscape in the Pittsburgh area and the best way to go about it. At the same time, it became clear that in order to grow and become as vibrant as the active leaders wanted to become, it would be best to end the formal relationship with CFI – Transnational. So in early 2017, the PA corporation Pittsburgh Freethought Community was formed and shortly after was granted 501(c)3 status by the IRS. In June, a letter was sent to CFI formally dissolving the chapter agreement and Pittsburgh Freethought Community took its place. Shortly afterward, the Humanist Community of Pittsburgh was formally merged into the new corporation, and the Meetup group, Steel City Skeptics was phased out at the end of 2017 (except for the blog).

The first officers of the PFC were Dana Morgenroth - President, Lizzie Vaughn - Vice President, Jacki Richey - Treasurer, and Victor Bernard - Secretary.

Since its founding, PFC has locally partnered with the First Unitarian Church of Pittsburgh and Sunday Assembly Pittsburgh.