Cockburn has written three books on Iraq. One, Out of the Ashes: The Resurrection of Saddam Hussein, was written with his brother Andrew Cockburn prior to the war in Iraq. The same book was later re-published in Britain with the title Saddam Hussein: An American Obsession. Two more were written by Patrick alone after the U.S. invasion, following his reporting from Iraq. The first, The Occupation: War and Resistance in Iraq (2006) mixes first hand accounts with reporting, Cockburn's book is critical of the invasion as well as the Salafi fundamentalists who comprise much of the resistance. The Occupation was nominated for the 2006 National Book Critics Circle award for nonfiction. The second, Muqtada: Muqtada al-Sadr, the Shia Revival, and the Struggle for Iraq was published in 2008. Muqtada is a journalistic account of the recent history of the religiously and politically prominent Sadr family, the rise of Muqtada, and the development of the Sadrist movementsince the 2003 U.S. invasion.
Cockburn's memoir is The Broken Boy (2005), a memoir of his childhood in 1950s Ireland, as well as an investigation of the way polio was handled – Cockburn himself caught and survived polio at the time. He has also published a collection of essays on the Soviet Union, titled Getting Russia Wrong: The End of Kremlinology (1989)and co-wrote the book Henry's Demons with his son, Henry which explains their coming to terms with the latter's diagnosis with schizophrenia. He also writes for CounterPunch and the London Review of Books.