Kanon was born in Pennsylvania and studied at Harvard University, and at Trinity College in Cambridge. As an undergraduate, he published his first stories in the The Atlantic Monthly. Later he became editor in chief, CEO, and president of the publishing houses Houghton Mifflin and E. P. Dutton in New York, before he began writing in 1995.

His first novel, Los Alamos (1997), became a bestseller and received the Edgar Award for Best First Novel in 1998. Further novels followed, including The Prodigal Spy, The Good German and Alibi. Kanon's stories are set in the period between World War II and 1950, and he has often used a real event, such as the Potsdam Conference or the Manhattan Project, as the background for a murder case. Kanon's novels are critically acclaimed, and reviewers from the Boston Globe and The New York Times have compared his work with the novels of Graham Greene and John le Carré . A film based on The Good German was produced in 2006, directed by Steven Soderbergh and starring George Clooney and Cate Blanchett.

Kanon lives with his wife, the literary agent Robin Straus, in New York City.