Cook was born and brought up in Buckinghamshire, England, UK. He received a B.A. (Hons) in Philosophy and Politics from Southampton University in 1987, a postgraduate diploma in journalism from Cardiff University in 1989, and an M.A. in Middle Eastern studies from the School of Oriental and African Studies in 2000.
Cook's career in journalism began in 1988 as a reporter and editor for regional newspapers the Southampton Advertiser and the Southampton Evening Echo. He was a freelance sub-editor with several national newspapers from 1994 until 1996. He was a staff journalist at The Guardian and staff at The Observer between 1996 and 2001.
Since September 2001, Cook has been a freelance writer based in Nazareth, Israel. He continued to write columns for The Guardian until 2007, and his articles have also been published in the The Observer, The International Herald Tribune, Le Monde Diplomatique, Al-Ahram Weekly, Al Jazeera,The National in Abu Dhabi, antiwar.com, CounterPunch.org, Dissident Voice, The Electronic Intifada, Modoweiss, AlterNet, among others.
Cook authored three books between 2006 and 2008. In Blood and Religion (2006), published by Pluto Press, the central thesis is that, "Israel is beginning a long, slow process of ethnic cleansing both of Palestinian non-citizens from parts of the occupied territories that it has long coveted for its expanded Jewish state, and of Palestinian citizens from inside its internationally recognized borders." Cook links this strategy to the Israeli perception of two threats: the physical threat of terrorism and the demographic threat of a Palestinian majority potentialized by high Palestinian birth rates and the continued demand for a Palestinian right of return. The Israeli leadership is also said by Cook to view the idea of a "state for all its citizens" as a threat. Rami George Khouri describes the short book as, "important but disturbing."
In 2008, Cook authored Israel and the Clash of Civilizations: Iraq, Iran and the plan to remake the Middle East, published by Pluto Press. Of the book, Antony Loewenstein notes that, "Cook bravely skewers the mainstream narrative of a Jewish state constantly striving for peace with the Palestinians." According to Lowenstein, Cook argues that Israel "pursues policies that lead to civil war and partition," and that this idea of dissolving many of the nations of the Middle East, shared by the neocons and the Bush administration, was developed by Israel's security establishment in the 1980s. Cook discusses an essay authored by Oded Yinon and published by the World Zionist Organisation in 1982 which advocated for Israel's transformation into a regional imperial power via the fragmentation of the Arab world, "into a mosaic of ethnic and confessional groupings that could be more easily manipulated" (p. 107). A review of the book in The Jordan Times calls it, "well-researched and very readable."
Disappearing Palestine: Israel's Experiments in Human Despair was published in 2008 by Zed Books. The book is in two parts, with the second half consisting of reprints of articles written by Cook as a journalist. The first half of the book, according to a review in Electronic Intifada, explores the thesis that, "the goal of Israeli policy is to make Palestine and the Palestinians disappear for good." Helena Cobban in the Boston Review says Cook argues that to encourage voluntary emigration, Israel has made life unbearable for Palestinians, primarily via "the ever more sophisticated systems of curfews, checkpoints, walls, permits and land grabs."
Cook is described by Neil Berry in the New Statesman as a writer of forensic rigour and a "maverick" journalist who chose to immerse himself in the culture that he writes about. According to Berry, he "exemplifies to an extreme degree the belief that when it comes to the Middle East, westerners of conscience are bound to be engaged with the Palestine/Israel conflict above all else. He regards Israel's treatment of the Palestinians as a monstrous injustice that must be resolved if stability is ever to be brought to the Middle East."