Nicknamed "Geno", Malkin began his career with his hometown club Metallurg Magnitogorsk, playing for their junior and senior teams.

[7] In November 2017, Malkin announced his membership of the PutinTeam social movement, launched by compatriot and fellow NHLer Alexander Ovechkin in support of President of Russia Vladimir Putin during the 2018 Russian presidential election.

In order to legally leave the team, on 15 August, Malkin invoked via fax a law allowing him to cancel his one-year contract by giving his employer two weeks' notice.

[16] In his first pre-season game with the Penguins, on 20 September 2006, Malkin collided with teammate John LeClair and dislocated his own shoulder, which forced him to miss the start of the season.

[19] Playing on a team with another highly touted prospect, sophomore forward and generational talent Sidney Crosby, Malkin finished his rookie season with 33 goals, 52 assists and 85 points in 78 games played, leading all first-year players and capturing the Calder Memorial Trophy as the NHL's top rookie, the second Penguin to win the award after Mario Lemieux in 1985.

When Malkin arrived in the United States, he spoke little English, but through the help of fellow Russian teammate Sergei Gonchar, he eventually started to give short, simple interviews in the language.

Malkin's sophomore season culminated in a Hart Memorial Trophy nomination as NHL MVP—the award was given to Ovechkin—and First team All-Star honours.

After having finished runner-up to Alexander Ovechkin the previous season for the Art Ross Trophy, Malkin captured the scoring championship with 113 points.

Malkin tallied 36 points (14 goals and 22 assists) to become the first player to lead both the regular season and playoffs in scoring since Mario Lemieux accomplished the feat in 1992.

[26] On 4 February 2011, after missing five games due to a left knee injury and sinus infection, Malkin returned to play against the Buffalo Sabres.

The Penguins estimated his recovery period as six months, sidelining him for the remainder of the 2010–11 season and playoffs, but stated he should be ready for training camp in mid-September.

"[28] In Malkin's absence, the Penguins as a team would end the season as the fourth seed in the Eastern Conference for the third straight season but their fortunes would change in the opening round of the 2011 playoffs against the Tampa Bay Lightning as the Penguins would lose in seven games to the fifth-seeded Lightning, despite initially having a 3–1 series lead earlier in the series.

With post-concussion syndrome limiting team captain Sidney Crosby to 22 games, Malkin led the Penguins on a line with newly acquired winger James Neal.

[31] Malkin would go on to win the Hart Trophy as the NHL's MVP for his performance in the season beating out Tampa Bay Lightning forward Steven Stamkos and New York Rangers goaltender Henrik Lundqvist, respectively.

[37] A concussion suffered on 22 February 2013 in a 3–1 win over the Florida Panthers after getting hit by Panthers defenseman Erik Gudbranson and a shoulder injury on 10 March in a 5–4 shootout win over the Toronto Maple Leafs caused by a hit by opposing forward James van Riemsdyk limited Malkin to 31 games during the season, rather than the 48 scheduled, in which he scored 33 points (nine goals, 24 assists).

The entire Penguins team was kept to two goals in the four-game series against the Bruins, with Malkin held off the scoresheet and posting a −5 plus-minus rating.

Malkin was unable to score for Pittsburgh in the first five games, and only managed four assists in that time, causing Penguins fans to worry, especially since Crosby was being held off the scoresheet as well.

On 30 October 2014, Malkin recorded his 400th assist on a Chris Kunitz goal in a 3–0 victory over the Los Angeles Kings to become the fifth player in franchise history to reach the mark.

On 17 February 2017, Malkin recorded his 500th career assist on a goal by Ian Cole in a 2–1 overtime loss to the Columbus Blue Jackets.

Despite this, he was able to finish the game recording two assists on goals by Phil Kessel and Kris Letang while also getting into a fight with Lightning forward and captain Steven Stamkos, which was later believed to have aggravated the injury.

[54] On 12 March, Malkin recorded his 1,000th NHL point on a Phil Kessel goal against the Washington Capitals, becoming the 88th player in league history to reach the mark.

He re-aggravated the injury in the season finale on 8 May in the Penguins 1–0 win over the Buffalo Sabres, causing him to miss the first two games in the opening round of the 2021 playoffs against the New York Islanders.

[59][60] On 11 April, Malkin was handed a four game suspension after he cross-checked Nashville Predators defenseman Mark Borowiecki the previous day and bloodying him.

On 12 July 2022, after initial reports that he would be heading to free agency, Malkin signed a four-year, $24.4 million contract extension to stay with the Penguins.

On 11 October 2024, Malkin recorded his 800th career assist on a goal by Erik Karlsson in a 6–3 win over the Detroit Red Wings, becoming the 34th player in league history to reach the mark.

[66] The following day, in a 4–2 loss to the Toronto Maple Leafs, Malkin recorded his 1,300th NHL point with an assist on a goal by Rickard Rakell, becoming the 37th player in league history to reach the mark.

The following year, Malkin finished second in team scoring at the 2005 World Junior Championships to Alexander Ovechkin with ten points.

Led by the duo of Malkin and Ovechkin (the two had also played together the previous year), Russia won the silver, losing to Canada in the gold medal game.

Following his NHL rookie campaign with the Pittsburgh Penguins, Malkin was named to the Russia squad for the 2007 World Championships, where he achieved a personal best for the tournament of ten points.

In 2019, Malkin played in the 2019 IIHF World Championship, where he recorded the primary assist on Russia's game-winning goal against Team USA in the knockout stage.