Macintyre is the author of a book on the gentleman criminal Adam Worth, The Napoleon of Crime: The Life and Times of Adam Worth, Master Thief. He also wrote The Man Who Would Be King: The First American in Afghanistan, and a book on the real-life double agent of Germany and England during the Second World War, Eddie Chapman, titled Agent Zigzag: The True Wartime Story of Eddie Chapman: Lover, Betrayer, Hero, Spy.

• Forgotten Fatherland: The Search for Elisabeth Nietzsche. New York: Farrar, Straus and Giroux, 1992. ISBN 978-0374157593.
• The Napoleon of Crime: The Life and Times of Adam Worth, Master Thief. New York: Farrar, Straus and Giroux, 1997. ISBN 978-0374218997.
• A Foreign Field. HarperCollins, 2001. ISBN 978-0002571227.
• The Englishman's Daughter: A True Story of Love and Betrayal in World War One. New York: Farrar, Straus and Giroux, 2002. ISBN 978-0374129859.
• The Man Who Would Be King: The First American in Afghanistan. New York: Farrar, Straus and Giroux, 2004. ISBN 978-0374201784.
• Agent Zigzag: The True Wartime Story of Eddie Chapman: Lover, Betrayer, Hero, Spy. London: Bloomsbury Publishing, 2007. ISBN 978-0747587941.

• The Last Word: Tales from the Tip of the Mother Tongue. London: Bloomsbury Publishing, 2009. ISBN 978-1408803332.
• Operation Mincemeat: The True Spy Story that Changed the Course of World War II. London: Bloomsbury Publishing, 2010. ISBN 978-0747598688.