Thurston, 27, had been heavily linked with a code switch, with teams in both Australia and Europe interested in offering him a lucrative deal to play rugby union.
But the scrum-half has opted to remain with the Cowboys, signing a deal until the end of 2013.
North Queensland executive director Peter Parr said: “I think it’s wonderful that Johnathan has decided to again re-sign with the Cowboys.
“He is without doubt one of the most exciting players in our game at the moment and to have him here in the North for the next three years is a great boost for our club and our game.”
Thurston has captained the Cowboys since 2006 and is one of the game’s true marquee players, with a playing record that includes 13 matches for Queensland (2005-09), 12 tests for Australia 2006-09, the 2008 World Cup and the Prime Minister’s XIII (2006, 2009).
The Cowboys have also retained the services of front-rower James Tamou for a further three years.
Parr added: “James Tamou is one of the best young forwards in Rugby League and to retain his services is also an important step for the Cowboys future.”