By 1973, demand had grown to the point where Fenway incorporated as a freestanding health center and sought a larger space at 16 Haviland Street.

The 16 Haviland Street location has since been closed as Fenway continues its attempts at reaching a broader audience than its traditional LGBT+ clients.

Fenway's involvement with advocacy and HIV/AIDS research led to its 1994 selection by the National Institute of Allergies and Infectious Diseases as one of eight sites recruiting participants for the first clinical trials of an HIV vaccine.

"We realized this was an important area that wasn't being covered," Dr. Steven Weinberger, senior vice president for medical education and publishing of the American College of Physicians, said in an interview at the time.

In December 2017, Fenway's CEO, Steven Boswell, resigned due to his handling of complaints about a prominent doctor who allegedly sexually harassed and bullied staff members of the health clinic.

[12] With the COVID-19 pandemic hitting soon after, Fenway removed the majority of medical and behavioral health appointments to telehealth, established testing programs in Boston and Everett, and activated several research studies, including COVID-19 vaccine trials.

Fenway Health's records are located in the Northeastern University Libraries, Archives and Special Collections Department, Boston, Massachusetts.