Farhana Khera received a bachelor's degree in 1991 from Wellesley College, where she served as president of the student body and co-founded a Muslim student organization called al-Muslimat (“The Muslim Women”). In 1994 she earned a JD from Cornell Law School, where she was an editor of the Cornell Journal of Law and Public Policy.
After completing her education, Khera worked as an associate at the law firms of Ross, Dixon & Masback (1994-96) and Hogan & Hartson (1997-99). After that, she spent five years as counsel to the U.S. Senate Judiciary Committee's Subcommittee on the Constitution, where she worked directly for Democratic U.S. Senator Russell Feingold, chairman of that Subcommittee. Under Feingold, Khera devoted much of her attention to the alleged inequities of the Patriot Act, racial and religious profiling, and other civil liberties issues raised by the federal government’s post-9/11 anti-terrorism policies.
Khera has been the executive director of Muslim Advocates since its founding in 2005. She also serves on the directors' board of the Alliance For Justice.
At a 2007 Islamic Society of North America (ISNA) convention, Khera condemned racial profiling and said: “We are concerned that if our law-enforcement officers are using stereotypes as a proxy for real evidence of criminal wrong doing, it’s not only wrong and non-American but an ineffective use of law enforcement resources.”
Also in 2007, Khera co-authored a memo that strongly influenced the decision by George Soros's Open Society Foundations to create a National Security and Human Rights Campaign (NSHRC) whose goals included:
On June 23, 2008, Muslim Advocates joined in a press release criticizing a Senate Homeland Security report which claimed that the threat from radical extremists was originating “increasingly from within” the United States. Khera, for her part, said that while the report “appropriately observes the value of outreach and engagement with American Muslims as vital to securing the freedom and safety of our nation, it undermines this very aim by falsely characterizing Muslims in America as susceptible to 'radicalization.'”
During the presidential administration of Barack Obama, Khera visited the White House on at least three separate occasions: February 2, 2010, when she met with Kaplen Modi, Associate Director of the Office of Public Engagement; March 1, 2011, when she met with Quintan Wiktorowicz, Senior Director for Global Engagement at the National Security Council; and August 1, 2011, when she met with Shaarik Zafar, Director for the Global Engagement Directorate at the White House National Security Staff.
In an April 13, 2010 article titled “Americans Should Be Free to Pray without FBI Snooping,” Khera: (a) accused the FBI of “planting informants” in “American Muslim congregations”; (b) claimed that FBI agents had infiltrated mosques all across the United States “without evidence of wrongdoing” in those places; (c) alleged that “the FBI also wanted to build a gym to attract young Muslims to work out and ‘discuss jihad’”; and (d) complained that the controversial Miami-based Imam, Foad Farahi of the Shamsuddin Islamic Center, “was threatened with deportation if he didn’t spy on his congregants.” As the Investigative Project on Terrorism notes, Imam Farahi is reported to have “links with known terrorists” including al-Qaeda operatives.
At a June 2010 hearing on “Racial Profiling and the Use of Suspect Classifications in Law Enforcement Policy,” Khera claimed that Muslim Americans in the post-9/11 era “have been subject to heightened scrutiny by federal law enforcement.” This scrutiny, she said, included “FBI interviews conducted in the community without suspicion of wrongdoing; extensive and invasive questioning and searches at the border; the surveillance of community organizations and the use of informants and undercover agents; and data gathering and mapping of the community based on cultural and ethnic behavior.”
At an ISNA convention in Chicago in July 2010:
At an annual dinner hosted by Muslim Advocates on December 10, 2010, Khera criticized U.S. government sting operations as a form of “entrapment” that unjustly targeted innocent Muslims with no real ties to terrorism. Moreover, she claimed that such operations fuel “anti-Muslim sentiment” while drawing public attention away from “actual threats.”
On October 19, 2011, Khera famously sent to then-Deputy National Security Adviser for Counterterrorism John Brennan, a letter demanding that all training materials and curricula for intelligence and counterterrorism agents be stripped of any “antiquated and offensive documents about Muslims and Islam” -- i.e., documents that made reference to “jihad” or “radical Islam.” The letter was signed by the leaders of 57 Muslim, Arab, and South Asian organizations in the United States, many of which had ties to Hamas and the Muslim Brotherhood. Among those signatories were ISNA, the Council on American-Islamic Relations, the Muslim American Society, the Islamic Circle of North America, Islamic Relief USA, and the Muslim Public Affairs Council. Within two weeks, Brennan capitulated to the letter's demand and called for a comprehensive purge of the offending items.
In February 2015, the Obama White House asked Khera to facilitate the first-ever roundtable meeting between Muslim community advocates and President Obama.
On December 29, 2016, Khera joined Alliance for Justice president Nan Aron in charging that President-elect Donald Trump's nominee for U.S. Attorney General, Senator Jeff Sessions, had “deep ties” to “the David Horowitz Freedom Center, which is on the Southern Poverty Law Center’s list of hate groups.” Specifically, Khera complained that Sessions had given speeches to the organization, and that he had received an award from “the anti-Muslim group” in 2014.
 Khera was Feingold's lead staff member for developing legislation against, and organizing subcommittee hearings on, racial profiling. Indeed, she wrote the first drafts of the End Racial Profiling Act and organized the first-ever Congressional hearing on racial profiling.