He was born in London, England, to an English father and American mother. He was raised in the Chicago area. Nolan attended Loyola Academy in Wilmette, Illinois, graduating in 1994, and then graduated from Georgetown University in Washington, D.C., in 1999, where he majored in English.

Nolan describes his successful working relationship with his brother in the production notes of The Prestige: "I’ve always suspected that it has something to do with the fact that he’s left-handed and I’m right-handed, because he’s somehow able to look at my ideas and flip them around in a way that’s just a little bit more twisted and interesting. It’s great to be able to work with him like that." In addition, they also contrast in the way they speak: both brothers have a mixed dialect of American and English, but Jonathan in a more American accent and Christopher in a more English accent. Jonathan Nolan Interview, The Prestige - MoviesOnline

On March 23, 2007, it was announced he would pen Interstellar, a science fiction film. It is based on the theories of Kip Thorne, a theoretical physicist known for his prolific contributions in gravitation physics and astrophysics and for having trained a generation of scientists. The film is being directed by Steven Spielberg and is scheduled to be released in 2013.

At a Comic Con press conference on July 26, 2008, Nolan was confirmed by director McG to be the "lead writer" of Terminator Salvation, Dark Knight Writer, Jonathan Nolan, Confirmed As “Lead Writer” of Terminator Salvation | /Film but was not listed under writing or story credits.

On February 9, 2010, it was revealed that Nolan is currently working with his brother and David S. Goyer on the third Batman film. It has also been reported that Nolan will be working on the next Superman film.