After nine months as a copy boy he started a journalism cadetship at the Gold Coast Bulletin, then in 1988 moved to The Courier-Mail in Brisbane. After a year, he moved to London as a foreign correspondent for News Limited Australia for two years. As a 22-year-old journalist there he covered historic events such as the fall of the Berlin wall and the Romanian Revolution.
Thomas returned to The Courier-Mail in late 1991, working there for 18 months. Thomas then moved to become the News Editor at the Hong Kong Standard for six months, before moving to the South China Morning Post in late 1993. There Thomas served in a variety of roles, including Senior Reporter, Deputy Features Editor, and Senior Writer.
In 1999 Thomas returned to Brisbane and The Courier-Mail.
In 2005 he won a Walkley award for a series of articles on Bundaberg Director of surgery Jayant Patel, which he later used a base for the non fiction book Sick to Death, published in 2007. The book also won the Queensland Premiers Literary Award for "Literary Work Advancing Public Debate".
In 2006 Thomas moved to the Brisbane bureau of The Australian, and in 2007 won a Gold Walkley for a series highlighting the flawed police pursuit of Mohamed Haneef, an innocent doctor accused of being a terrorist. After winning the award, Thomas left journalism in early 2008 to work in the resources sector, with a role in communications, investor and government relations.
Thomas won a second Gold Walkley in 2018, along with producer Slade Gibson, for podcast series The Teacher's Pet, a 14-episode investigation of the unsolved case of missing Sydney mother Lyn Dawson from 1982. It was downloaded by 27 million listeners across the world, and was the only Australian podcast to hit the number one spot in the US, the UK, Canada and New Zealand.
- 1999 Walkley for Best Investigative Writing (with Paul Whittaker) for exposing the "Net Bet affair".
- 2003 Walkley for Best Print Feature, "Court in Crisis" on Di Fingleton, jailed Chief Magistrate of Queensland.
- 2005 Walkley for Best Print News story, "Exposing a Sick System" regarding Dr Jayant Patel, Bundaberg Director of Surgery.
- 2005 Sir Keith Murdoch Award, for the Patel story.
- 2007 Walkley for Best Print New story, for the Mohamed Haneef story. and Gold Walkey.
- 2012 Queensland Clarion Award for Best Investigative 2012 for highlighting evidence overlooked by the judicial inquiry into the operation of the Wivenhoe Dam during the 2011 Queensland floods
- 2012 Queensland Clarion Award for Journalist of the Year
- 2012 received an Honorary Doctorate of Journalism from John Henningham's Jschool School of Journalism in Brisbane.
- 2018 Gold Walkley for The Teachers Pet Podcast.
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- "Scandal-mongering or good reporting?". ABC Media Watch. 27 August 2012. Retrieved 14 January 2017.
- Hedley Thomas, Slade Gibson win Gold Walkley for true crime podcast, ABC News Online, 2018-11-23
- Cockburn, Paige; Sas, Nick (6 December 2018). "The power of the podcast — in Lynette Dawson's case was it a help or hindrance?". ABC News. Retrieved 3 January 2019.
- Mediaweek (19 November 2018). "More media greats inducted into Australian Media Hall of Fame". Mediaweek. Retrieved 14 January 2019.
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- "Hedley Thomas". The Walkley Foundation. Archived from the original on 5 February 2013. Retrieved 19 September 2012.
- "Haneef story gets Thomas a Gold Walkley". Sydney Morning Herald. 29 November 2007. Retrieved 14 January 2019.
- "2012 Queensland Clarion Awards". clarions.org. Retrieved 3 September 2012.
- "Fairfax in talks". The Australian. 22 October 2012.