Thayer’s reporting has earned him The World Press Award, the 1997 British Press Awards 2006 Scoop_of_the_Year British Press Award, and the 1998 Francis Frost Wood Award for Courage in Journalism, given by to a journalist "judged to best exemplify physical or moral courage in the practice of his or her craft."
He was a visiting scholar at the Paul H Nitze School of Advanced International Studies at Johns Hopkins University
He was the recipient of the Center for Public Integrity International Consortium of Investigative Journalists (ICIJ) Award for Outstanding International Investigative Reporting oof the Year (http://www.publicintegrity.org/investigations/icij http://www.publicintegrity.org/investigations/icij/journalists/profile/856/ "Upon awarding Thayer the ICIJ Award, the judges noted: :"He illuminated a page of history that would have been lost to the world had he not spent years in the Cambodian jungle, in a truly extraordinary quest for first-hand knowledge of the Khmer Rouge and their murderous leader. His investigations of the Cambodian political world required not only great risk and physical hardship but also mastery of an ever-changing cast of Political faction characters." http://www.publicintegrity.org/assets/pdf/pi_1999_03.pdf Maud S. Beelman, "Reporting Across Borders," The Public i: Newsletter of the Center for Public Integrity,Vol 7, no. 2, Mar 1999.]
According to Vaudine England of the BBC "Many of the regions greatest names in reporting made their mark in the pages of the Far Eastern Economic Review from the legendary Richard Hughes of Korean War fame, to Nate Thayer, the journalist who found Cambodias Khmer Rouge leader Pol Pot."http://news.bbc.co.uk/2/hi/asia-pacific/8268105.stm Vaudine England, "Leading Asian Magazine to Close," BBC Asia-Pacific News, September 22, 2009.]
Thayer was also the first person in 57 years to turn down a prestigious Peabody Award because he did not want to share it with ABC News [Nightline] saying publicly lambasting American television news saying:"I in no way want my name associated with such egregious violations of journalistic and professional ethics." .http://www.independent.co.uk/news/media/your-scoop-nah-its-ours-if-we-want-it-1157187.html "Your scoop? Nah. Its ours if we want it." The Independent May 25 1998.]
Thayer is also the recipient of The Overseas Press Club of America Award, as well as the Asian Society of Publishers and Editors Award for "Excellence in Reporting,"
Thayer was also honored with the SAIS-Novartis "Award for Excellence in International Reporting."
He was nominated for a Pulitzer Prize by The Wall Street Jounral
In 1999 Thayer established at the Hofstra Universitys Department of Journalism and Mass Media Studies in the School of Communication the Nate Thayer Scholarship given annually to "a qualified student with the best foreign story idea. Winners are selected on the basis of scholastic achievement or potential as well as economic need." http://www.hofstra.edu/pdf/1999/ho019900008.pdf Hofstra University Student Information Package, Financial Aid Section, p. 45.] http://www.hofstra.edu/Academics/Colleges/SOC/JMSPR/index.html