The organization's board of directors has included well-known journalists and whistleblowers such as Daniel Ellsberg, Laura Poitras, Glenn Greenwald, and Xeni Jardin, as well as activists, celebrities, and filmmakers. NSA whistleblower Edward Snowden joined FPF’s board of directors in 2014 and began serving as its president in early 2016. Jardin left the board in 2016.
FPF’s mission includes "promoting and funding aggressive, public-interest journalism focused on exposing mismanagement, corruption, and law-breaking in government", and runs crowd-funding campaigns for independent journalistic organizations.
The organization’s founding was inspired by the WikiLeaks financial blockade. When FPF launched in late 2012, it was the first time people could donate to WikiLeaks via Visa, MasterCard, and PayPal since the payment processors cut off WikiLeaks in late 2010. In December 2017, after five years of processing donations on behalf of WikiLeaks, FPF's board unanimously found that the blockade was no longer in effect, and severed ties with WikiLeaks as of January 8, 2018.
FPF has also crowd-funded support for a variety of other transparency journalism organizations, as well as encryption tools used by journalists, including: WikiLeaks, MuckRock, the National Security Archive, The UpTake, The Bureau of Investigative Journalism, the Center for Public Integrity, Truthout, the LEAP Encryption Access Project, Open Whisper Systems, Tails, and the Tor Project.
In May 2013, FPF raised over $100,000 online donations to hire a professional court stenographer to take transcripts during the trial of whistleblower Chelsea Manning after the government refused to make its transcripts available to the public. They posted the transcripts online at the end of each day of the trial for members of the media to use in their reports. Secrecy expert Steven Aftergood later called the crowd-funding effort "unprecedented," saying "it eloquently demonstrated public expectations of openness...the court and the prosecutors may have been shamed into reconsidering their habitual secrecy." 
In October 2014, FPF raised over $28,000 for New Zealand independent journalist Nicky Hager to fund his legal challenge against the government of New Zealand after his house was raided by police following a book he wrote. A court later ruled the raid of Hager’s house was illegal.
In 2015, FPF raised more than $125,000 online for Chelsea Manning’s legal defense stemming from her conviction under the Espionage Act for leaking information to WikiLeaks. Notwithstanding the January 2017 commutation of her sentence and May 2017 release from prison, Manning's military appeal is ongoing.
In October 2013, FPF took over the development of SecureDrop, an open source whistleblower submission system developed in part by the late programmer and transparency activist Aaron Swartz., who developed it with Kevin Poulsen and James Dolan. Dolan moved it to FPF upon the death of Swartz. The SecureDrop system facilitates anonymous communication between two parties using the Tor Network, and allows whistleblowers to contact journalists without ever exchanging one another's identities or contact information.
The system is now is in use at over two dozen major news organizations, including The Washington Post, The Guardian, The New Yorker, ProPublica, Gawker, HuffPost, and The Intercept. According to a study done by Columbia Journalism School, it has since successfully led to the publication of many stories at the news organizations that use it.
FPF also teaches journalists how to use other encryption and digital security tools to better protect their sources.
Freedom of the Press Foundation has been involved in several Freedom of Information Act cases surrounding journalists’ rights and government transparency.
In January 2016, FPF’s lawsuit against the Justice Department revealed that the US government has secret rules for targeting journalists with National Security Letters (NSLs) and FISA court orders.
In March 2016, another FPF lawsuit showed that the Obama administration secretly lobbied against bipartisan Freedom of Information Act reform in Congress, despite the bill being based word-for-word on the Obama administration’s supposed transparency guidelines.
FPF co-founders Daniel Ellsberg, John Perry Barlow, Trevor Timm, and Rainey Reitman won the 2013 Hugh Hefner First Amendment award for their role in founding FPF. The organization was the recipient of the Society of Professional Journalists’ James Madison award in 2016.