He studied Arabic studies at the University of Westminster and Latin (BA Hons) at the University of Birmingham. A former joint investigations editor of The Sunday Times, he left the title at the time of the Wapping dispute. For a period during 1987, he was editor of the short-lived News on Sunday tabloid. The newspaper published extracts from Spycatcher by Peter Wright in August 1987 while Whitaker was editor. The title was eventually fined £50,000 in May 1989 for contempt of court in breaking an injunction upheld by the Law Lords shortly before publication.
Whitaker worked for the British newspaper The Guardian from 1987 and was its Middle East editor from 2000 to 2007. He runs a personal, non-Guardian-related website, Al-Bab.com, about politics in the Arab world.
- News Limited: Why You Can't Read All About it, 1981 (London: Minority Press Group) ISBN 978-0-906890-03-5, ISBN 978-0-906890-04-2, OCLC 8229010
- Notes and Queries, vol. 1-5, 1990 (London: Fourth Estate) ISBN 978-1-872180-22-9, OCLC 22182928, a collection of Q&A from the readers of The Guardian
- Unspeakable Love: Gay and Lesbian Life in the Middle East, 2006 (London: Saqi Books) ISBN 978-0-86356-819-0, (Berkeley:University of California Press) ISBN 0-520-25017-6, OCLC 238877880
- What's "Really" Wrong with the Middle East?, 2009 (London: Saqi Books) ISBN 978-0-86356-624-0, OCLC 416261943
- Arabs Without God: Atheism and Freedom of Belief in the Arab World, 2014 (CreateSpace) ISBN 9781501064838
- "Whitaker, Brian 1947–". Encyclopedia.com. Retrieved 19 September 2021.
- "Bitter battle at Wapping: scenes at the frontline". Press Gazette. 19 January 2006. Retrieved 19 September 2021.
- Greenslade, Roy. Press Gang: How Newspapers Make Profits from Propaganda. London: Pan Macmillan. p. 494–495.
- "Britain to Punish Paper in Spy Case". The New York Times. Reuters. 5 August 1987. Retrieved 19 September 2021.
- "Government to Prosecute Newspaper for Printing Spy Book Exerpts". AP News. 5 August 1987. Retrieved 19 September 2021.
- "Papers fined £150,000 for Spycatcher contempt". The Glasgow Herald. 9 May 1989. Retrieved 19 September 2021.