He most recently faced consistent challenger Pat Healy, as a replacement for Thomson's original opponent Lyle Beerbohm. The fight was close, with Healy winning the first two rounds after breaking Thomson's ribs with his very first takedown but falling to a rear-naked choke from Thomson in the last minute of the fight.
Thomson next fought Gesias Cavalcante in "JZ"'s Strikeforce debut. Thomson won a highly controversial unanimous decision in what was nonetheless a great fight. With the victory, he earned a third shot at lightweight champion Gilbert Melendez in what would be a highly anticipated rubber match certainly. It was unknown when this match would take place since Thomson faced a 180-day suspension following the Cavalcante fight due to a serious hand and knee injury combination.
Thomson instead faced well-rounded veteran Tatsuya Kawajiri at the end-of-the-year Dynamite show in what was sure to be a slugfest. Kawajiri defeated Thomson via unanimous decision. He was next set to face young debuting prospect Maximo Blanco. Unfortunately Thomson was injured and forced to pull out. He was replaced by Pat Healy.
After recovering, Thomson signed to face former EliteXC lightweight champion and former boxer KJ Noons. He defeated Noons via a lackluster but dominant unanimous decision. With the victory, Thomson earned the possible final shot for the Strikeforce lightweight championship in a rubber match against champion and rival Gilbert Melendez.
The rubber match occurred with Melendez winning a controversial split decision victory. After Strikeforce's roster was liquidated into the UFC in January 2013, Thomson's contract went with it.
Thomson signed to make his return against UFC lightweight standout Nate Diaz. Thomson gave Diaz one of the worst beatings of his career en route to an impressive second round technical knockout victory.
Thomson was next rumored to either face UFC veteran Diego Sanchez or fight a rematch against fellow Strikeforce veteran Pat Healy. Thomson was also called out by mid-level (at best) featherweight fighter Cody McKenzie.
Thomson himself then called out former WEC lightweight champion and contender Anthony Pettis. The fight materialized in a very unexpected way after Pettis defeated champion Ben Henderson for the UFC lightweight title and Thomson stepped in to replace contender TJ Grant for a shot at the title in January 2014.
Instead Pettis was replaced by former UFC lightweight champion Ben Henderson. The winner would receive a shot against Pettis in the early summer 2014. Henderson won an extremely controversial and close split decision over Thomson who contemplated retirement afterwards.
After some time off and recovery from an injury cancellation against Gilbert Burns, Thomson signed to fight prospect Tony Ferguson. Ferguson ended up beating a game Thomson up en route to a dominant and bloody unanimous decision.
With the third straight loss Thomson's UFC contract was up and the UFC declined to match an offer from rival Bellator, leading to Thomson signing with Bellator which was run by former Strikeforce frontman Scott Coker.
Thomson soon signed to make his Bellator debut against former LFC champ Mike Bronzoulis.
- Josh Thomson vs. Rob McCullough
- Josh Thomson vs. Gerald Strebendt - The fight was Thomson's UFC debut.
- Josh Thomson vs. Hermes Franca - Hermes Franca came into the fight undefeated and it was his first career defeat.
- Yves Edwards vs. Josh Thomson - The fight was one of the sport's first true highlight-reel knockouts. The fight was Thomson's first loss and his last UFC fight as of 2011.
- Josh Thomson vs. Daisuke Sugie - The fight was Thomson's Pride debut and his only fight with the promotion.
- Josh Thomson vs. Harris Sarmiento
- Josh Thomson vs. Nam Phan - The fight was for the "Strikeforce U.S. lightweight championship" which Thomson defended once before it became defunct.
- Gesias Cavalcante vs. Josh Thomson - The fight and its controversial decision was the Strikeforce debut of Gesias Cavalcante.
- Tatsuya Kawajiri vs. Josh Thomson - The fight was Josh Thomson's Dream debut.
- Josh Thomson vs. Mike Bronzoulis - The fight was Thomson's Bellator debut.
- Josh Thomson vs. Pablo Villaseca