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In February 2019, Zittrain interviewed Facebook CEO Mark Zuckerberg as part of a seminar for students at Harvard.

In 2009 Zittrain was elected to the Internet Society's board of trustees for a four-year term. In February 2011 he joined the board of the Electronic Frontier Foundation. In May 2011 Zittrain was made for Federal Communications Commission Distinguished Scholar. In May 2012 he was made for Chair at Federal Communications Commission Open Internet Advisory Committee.

He has been critical of the process used by ICANN, the International Telecommunication Union and the World Summit on the Information Society. Although he describes their approach as, in some ways, simple and naïve, Zittrain sees more hope in the open Internet Engineering Task Force model and in the ethical code and assumption of good faith that govern Wikipedia. He wrote in 2008, "Wikipedia—with the cooperation of many Wikipedians—has developed a system of self-governance that has many indicia of the rule of law without heavy reliance on outside authority or boundary."

Reactions in the Boston Review accompanied the publication of his book, The Future of the Internet and How to Stop It, in 2008. Support came from David D. Clark and Susan P. Crawford. Criticism ranged from Richard Stallman's finding no evidence of a flight to closed systems and his message that software developers need control and software patents must end, to a request for cost-benefit analysis, to the belief that netizenship won't scale to the business world to faith that consumers will buy only open, non-proprietary systems.

Writing with Laura Freider of Purdue University, in 2008 Zittrain published Spam Works: Evidence from Stock Touts and Corresponding Market Activity, in the Hastings Communications and Entertainment Law Journal to document the manipulation of stock prices via spam e-mail. They found evidence that "stocks experience a significantly positive return on days prior to heavy touting via spam" and that "prolific spamming greatly affects the trading volume of a targeted stock". Apart from transaction costs, in some circumstances the spammer earned over 4% while the average investor who bought on the day of receipt of the spam would lose more than 5% if they sold two days later. Frieder said in 2006 that she knew of no other explanation for their results, but that people do follow the stock tips in their spam e-mail.

One of StopBadware's goals is to "preempt" the stifling of the Internet. The founders think that centralized regulation could follow a serious Internet security breach, and that consumers might then choose to purchase closed, centrally managed solutions like tethered appliances that are modified by their vendor rather than owner, or might flee to services in walled gardens. In Zittrain's word, "generative" devices and platforms, including the Internet itself, offer an opening forward. In 2007, he cautioned, "...we're moving to software-as-service, which can be yanked or transformed at any moment. The ability of your PC to run independent code is an important safety valve."

After Zittrain joined the staff at Oxford, Zittrain and John Palfrey at the Berkman Center founded StopBadware.org in 2006 to function as a clearinghouse for what has become proliferation of malware. Borrowing Wikipedia's "ethical code that encourages users to do the right thing rather than the required thing", the organization wished to assign the task of data collection—and not analysis—about malware to Internet users at large. When its scans find dangerous code, Google places StopBadware alerts in its search results and rescans later to determine whether a site thereafter had been cleaned.

Zittrain joined the staff of the University of Oxford in Oxford in the United Kingdom as of September 2005. He held the Chair in Internet Governance and Regulation, was a principal of the Oxford Internet Institute, and was a Professorial Fellow of Keble College, which has developed a particular interest in computer science and public policy. In the United States, he was also the Jack N. & Lillian R. Berkman Visiting Professor for Entrepreneurial Legal Studies at Harvard Law School in Cambridge, Massachusetts and director and founder with Charles Nesson of its Berkman Center for Internet & Society. Zittrain was a visiting professor at the Stanford Law School in 2007 and was a visiting professor at New York University School of Law in Manhattan for the spring 2008 semester.

Zittrain is the son of two attorneys, Ruth A. Zittrain and Lester E. Zittrain. In 2004 with Jennifer K. Harrison, Zittrain published The Torts Game: Defending Mean Joe Greene, a book the authors dedicated to their parents. His brother, Jeff, is an established Bay Area musician. His sister, Laurie Zittrain Eisenberg, is a scholar of the Arab and Israeli conflict and teaches at Carnegie Mellon University in Pittsburgh.

Building on the work completed at the Berkman Center, ONI published special reports, case studies, and bulletins beginning in 2004, and as of 2008, offered research on filtering in 40 countries as well as by regions of the world. As of 2016, Zittrain remains a principal investigator at ONI, together with Ronald Deibert of the University of Toronto, John Palfrey, who was previously the executive director of the Berkman Center (now the head of School at Phillips Academy in Andover, Massachusetts), and Rafal Rohozinski of the University of Cambridge.

On October 9, 2002, Zittrain and Lawrence Lessig argued a landmark case, known as Eldred v. Ashcroft, before the United States Supreme Court. As co-counsel for the plaintiff, they argued that the Sonny Bono Copyright Term Extension Act (CTEA) was unconstitutional. The court ruled 7–2 on January 15, 2003 to uphold the CTEA which extended existing copyrights 20 years, from the life of the author plus 50 years, to plus 70 years. In the words of Justice Ruth Bader Ginsburg, the petitioners did "not challenge the CTEA's 'life-plus-70-years' time span itself. They maintain that Congress went awry not with respect to newly created works, but in enlarging the term for published works with existing copyrights." The court found that the act did "not exceed Congress' power" and that "CTEA's extension of existing and future copyrights does not violate the First Amendment". In 2003 Zittrain said he was concerned that Congress will hear the same arguments after the 20-year extension passes, and that the Internet is causing a "cultural reassessment of the meaning of copyright".

Zittrain works in several intersections of the Internet with law and policy including intellectual property, censorship and filtering for content control, and computer security. He founded a project at the Berkman Klein Center for Internet & Society that develops classroom tools. In 2001 he helped found Chilling Effects, a collaborative archive created by Wendy Seltzer to protect lawful online activity from legal threats. He also served as vice dean for Library and Information Resources at Harvard.

The OpenNet Initiative (ONI) monitors Internet censorship by national governments. Between 2001 and 2003 at Harvard's Berkman Center, Zittrain and Benjamin Edelman studied Internet filtering. In their tests during 2002, when Google had indexed almost 2.5 billion pages, they found sites blocked, from approximately 100 in France and Germany to 2,000 in Saudi Arabia, and 20,000 in the People's Republic of China. The authors published a statement of issues and a call for data that year.

In 2001, Zittrain cofounded Chilling Effects with his students and former students, including its creator and leader, Wendy Seltzer. It monitors cease and desist letters. Google directs its users to Chilling Effects when its search results have been altered at the request of a national government. Since 2002, researchers have been using the clearinghouse (renamed "Lumen" in 2015) to study the use of cease-and-desist letters, primarily looking at DMCA 512 takedown notices, non-DMCA copyright, and trademark claims.

He was law clerk for Stephen F. Williams of the United States Court of Appeals for the District of Columbia Circuit and served with the U.S. Department of Justice and, in 1991, with the Department of State, as well as at the Senate Select Committee on Intelligence in 1992 and 1994. He was a longtime forum administrator, or sysop, for the online service CompuServe, serving for many years as the chief administrator for its private forum for all of its forum administrators.

Zittrain, who grew up in the suburb of Churchill outside of Pittsburgh, graduated in 1987 from Shady Side Academy, a private school in Pittsburgh, Pennsylvania. He holds a bachelor's summa cum laude in cognitive science and artificial intelligence from Yale University, 1991, where he was a member of the Yale Political Union, Manuscript Society and Davenport College, a J.D. magna cum laude from Harvard Law School, 1995, where he was the winner of the Williston Negotiation Competition, and a master of public administration from Harvard's John F. Kennedy School of Government, 1995.

Jonathan L. Zittrain (born 24 December 1969) is an American professor of Internet law and the George Bemis Professor of International Law at Harvard Law School. He is also a professor at the Harvard Kennedy School, a professor of computer science at the Harvard School of Engineering and Applied Sciences, and co-founder and director of Harvard's Berkman Klein Center for Internet & Society. Previously, Zittrain was Professor of Internet Governance and Regulation at the Oxford Internet Institute of the University of Oxford and visiting professor at the New York University School of Law and Stanford Law School. He is the author of The Future of the Internet and How to Stop It, as well as co-editor of the books, Access Denied (MIT Press, 2008), Access Controlled (MIT Press, 2010), and Access Contested (MIT Press, 2011).