The 30-year-old Queenslander was man-of-the-match in the Kangaroos’ World Cup final victory, and in several games in the lead-up, beat England and South Sydney prop Sam Burgess.
The award is voted by a 13-man expert panel, who placed New Zealand’s Sonny Bill Williams in third – the dual code international star won the Rugby League International Federation’s player of the year award.
Fourth and fifth were Australia captain Cameron Smith and Scotland skipper Danny Brough, the Super League’s 2013 Man of Steel.
“We asked the panel to consider performances in international matches first and foremost and, given his outstanding World Cup campaign, Jonathan Thurston has emerged as a deserving winner,” Rugby League World editor Gareth Walker said.
“It was typical of the way he orchestrated his Australian side superbly in the match that mattered most, though it should be noted that he was excellent for the entire competition.
“Ever since breaking onto the international scene almost eight years ago, Thurston has been at the very forefront of the sport at its highest level.”
Andrew Johns and Darren Lockyer are the only others who have won the Golden Boot twice.
A World 13 was also named by Rugby League World and it was dominated by Australia with two each from England and New Zealand – all players in the line-up are from the NRL.
Billy Slater, Roger Tuivasa-Sheck (NZ), Greg Inglis, Jamie Lyon, Brett Morris, Jonathan Thurston, Cooper Cronk, Sam Burgess (England), Cameron Smith, James Graham (England), Sonny Bill Williams (NZ), Greg Bird, Paul Gallen.
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