[4][5] In 2006, Khudobin returned to Russia and took over back-up goaltending duties for Metallurg in the Russian Superleague (RSL), helping the team to the league championship.

[18] His early start with the team began slowly after suffering an ankle injury on 13 October against the Phoenix Coyotes, resulting in a temporary conditioning stint in the AHL.

"[24] On 27 June 2015, the second day of the 2015 NHL Entry Draft, Khudobin was traded to the Anaheim Ducks in exchange for defenceman James Wisniewski.

[28] He played in eight games for the Ducks, posting a 3-3-0 record and 2.70 goals-against average, before being reassigned to their AHL affiliate, the San Diego Gulls on 15 December.

[29] During his reassignment to the Gulls, Khudobin posted a 4-4-1 record with a 2.60 GAA and .911 SV% in eight games before earning his first recall on 17 January 2016 to replace an injured Clayton Stoner.

[31] As a free agent at the conclusion of the 2015–16 season with the Ducks, on 1 July 2016, Khudobin signed a two-year contract to return to the Boston Bruins.

[32] He began the season as Rask's backup but after the former suffered an injury, he started two games for the team and posted a 0–2–0 record with a .849 save percentage and 4.10 GAA.

Although he missed practice, coach Bruce Cassidy said it was "nothing major" and he was expected to start in net by the final preseason game against the Chicago Blackhawks.

[34] On 1 July 2018, Khudobin joined his fifth NHL club as a free agent, agreeing to a two-year, $5 million contract to assume backup duties for the Dallas Stars.

When speaking of the addition, General Manager Jim Nill spoke highly of the goaltender saying "Anton is a proven NHL netminder that gives his team a chance to win every time he's on the ice...We look forward to him joining our club and making a positive impact for the next two seasons.

[36] During the pre-season, Khudobin split his time in net with rookie goaltender Colton Point who was making his NHL debut out of college.

[39] As the Stars pushed to qualify for the 2019 Stanley Cup playoffs, both Khudobin and Ben Bishop were praised for their goaltending abilities by coach Jim Montgomery.

On 13 December 2021, with the goalie tandem of Braden Holtby and Jake Oettinger providing stellar play in net, the Stars waived Khudobin with two years and $7.05 million guaranteed left on his contract.

[45] On 2 March 2023, the Stars traded Khudobin along with a second-round pick in the 2025 NHL Entry Draft to the Chicago Blackhawks in exchange for Max Domi and Dylan Wells.

[46] Having concluded his contract with the Blackhawks, Khudobin signed as a free agent with Russian second tier club, Sokol Krasnoyarsk of the VHL, on 5 September 2023.