Johanna Fernández was born on December 2, 1970, in The Bronx, New York. Her parents, Tirso Apolinar Fernández Sr. and Minerva Estevez, immigrated to the United States from the Dominican Republic in the late 1960s. She is one of four children.

Fernández began high school at Murry Bergtraum High School for Business Careers, but transferred to the Manhattan Center for Science and Math in her junior year. There, she was admitted to the Double Discovery Program at Columbia, a college preparation program for poor and working class communities of color in urban centers. She completed her senior year of high school and completed her A-levels in Godalming, England, through a program organized by the British American Educational Foundation.

After deferring her admission for one year, Fernández entered Brown University in 1989 where she earned her undergraduate degree in Literature and American Civilization in 1993. During her time there, she became a key organizer of the student group SAMA – Students for Admissions and Minority Aid, which led the April 1992 student occupation of University Hall in hopes of pressuring Brown to move more rapidly towards need-blind admissions. During the takeover, 253 students, including Fernández, were arrested and charged with felonies for not vacating University Hall. Need-blind admissions would not be established at Brown until 2003 and was not fully practiced until 2007.

Fernández continued her education at Columbia University where she received her PhD in history in 2004. Her dissertation, , focuses on the history of the Young Lords Party – the Puerto Rican counterpart to the Black Panther Party – through their major campaigns and political world view. While earning her PhD, Fernández taught at the Brooklyn Institute of Technology (1998-1999), Columbia University (1999), and Trinity College (2002-2005). After graduating, she was a postdoctoral fellow at Carnegie Mellon University (2005-2007) and is currently Associate Professor of history at Baruch College in the City University of New York, where she teaches 20th Century US history and the history of social movements.

It was during Fernández's time at Carnegie Mellon University, located in Pittsburgh, PA, when she met a professor and civil rights activist named David P. Demarest, and Martha Conley, the first Black woman to graduate from the University of Pittsburgh Law School and Bariki Hall, and Mumia Abu-Jamal's music teacher. Both urged Fernández to become more intimately involved in Abu-Jamal's case as she had already participated in part of the world movement that stopped his ececution in the 1990s. All three were members of the Pennsylvania Prison Society and visited men on death row often.

Fernández sent her first letter to Mumia in 2006 and visited him in person for the first time during this same period. Over time, the two developed a bond that led to Fernández becoming one of Abu-Jamal's lead advocates, successfully working to get him off of death row and continuing to work on his release from prison. She became involved in the Free Mumia Movement and currently heads one if its key organizations, the Campaign to Bring Mumia Home. In 2010, she wrote and produced the documentary . In 2014, the two co-edited a special issue of the journal , titled "The Roots of Mass Incarceration in the US: Locking Up Black Dissidents and Punishing the Poor." And in 2015, Fernández edited by Abu-Jamal. She also routinely includes recordings and live calls with Abu-Jamal in her courses.

While heading advocacy work for and with Abu-Jamal, Fernández continued her research on the Young Lords. In 2014, she sued the New York Police Department (NYPD) for its failure to honor her research-driven, Freedom of Information Law (FOIL) request. Her suit led to the recovery of the "lost" Handschu files, the largest repository of police surveillance documents in the country. The collection includes over one million surveillance files of New York political organizations compiled by the NYPD between 1954-1972, including those of the Black Panthers, the Nation of Islam, and the Young Lords, as well as public demonstrations and civil unrest. After Fernández identified that the correct files were recovered, she spent months writing a grant for the Mellon Foundation to have the files digitized out of concern that they would not be properly cared for. The grant was awarded for a half million dollars but the municipal archive housing the documents declined to accept.

Using the Handschu files, as well as original oral histories and archival collections, Fernández published in 2020. This definitive account of the Young Lords chronicles their roots as a Chicago street gang to their rise and fall as a political organization in New York. It has earned the American Book Award and the New York City Book Award, as well as the three top awards of the Organization of American Historians, including the prestigious Frederick Jackson Turner award for best first book in history.

Fernández's overall work has also earned several awards including a National Endowment for the Humanities Fellowship of the Scholars-in-Residence program at the Schomburg Center for Research in Black Culture of the New York Public Library (2007) and the Fulbright Scholars grant to the Middle East and North Africa (2011), which took her to Jordan. In 2015, she directed and co-curated "¡Presente! The Young Lords in New York," an exhibition in three New York City museums cited by as one of the year's "Top 10, Best In Art." Her mainstream writings have been published internationally, from to the . She has appeared in a diverse range of print, radio, online and televised media including NPR, , the , and Democracy Now!.

To learn more about Fernández, listen to oral history interviews she contributed to the Pembroke Center Oral History Project.