Nikishin's first season in the NHL was a memorable one.

He became a Stanley Cup champion with the Carolina Hurricanes following their six-game win against the Vegas Golden Knights. He was named to the 2025-26 NHL All-Rookie Team, the third-round pick (No. 69) in the 2020 NHL Draft ranking second among first-year defensemen with 33 points (11 goals, 22 assists) in 81 games. Nikishin's 11 goals set a Hurricanes/Hartford Whalers record for a rookie at his position ahead Justin Faulk's eight in 66 games of the 2011-12 season and his 33 points were second to Brad Shaw's 35 for the Whalers in 1989-90. He joined three other defensemen, Chris Pronger (1993-94), Shaw (1989-90) and Dana Murzyn (1985-86) to receive the honor while the franchise was in Hartford.

Nikishin signed a two-year, $1.665 million entry-level contract with the Hurricanes on April 11, 2025, after he had 46 points (17 goals, 29 assists) in 61 regular-season games as captain for SKA St. Petersburg of the Kontinental Hockey League in 2024-25, ranking second among KHL defensemen in goals and game-winning goals (four) and third in points. He left Russia as SKA's all-time leader in points by a defenseman (177; 54 goals, 123 assists) and 15 points (eight goals, seven assists) in 35 playoff games. His 55 points (11 goals, 44 assists) set a single-season scoring record by a KHL defenseman born in Russia, which he broke the following season with 56 points (17 goals, 39 assists).

Nikishin was named KHL Defenseman of the Month seven times in three seasons and won a silver medal while he was Russia's youngest player at the 2022 Beijing Olympics.