Niskanen attended the University of Minnesota Duluth. At the 2005 NHL Entry Draft, he was selected in the first round, 28th overall, by the Dallas Stars. In 2005-06, his freshman season for the Bulldogs men's ice hockey team, he recorded 14 points in 38 games. Before that, Niskanen played for the Virginia/Mountain Iron-Buhl boys' hockey team and helped bring the Blue Devils to their first state high school tournament appearance in school history. During 2006–07, his sophomore season at UMD, he scored 9 goals and 22 assists in 39 games. Niskanen was named to the 2006–07 All WCHA First Team, and the All WCHA academic Team. Niskanen decided to leave college and turn professional after his sophomore season at UMD. On March 19, 2007, he signed an amateur tryout contract with the Iowa Stars—the Dallas Stars' American Hockey League affiliate at the time—for the remainder of the 2006–07 season. He later signed a three-year NHL contract with the Dallas Stars which began in 2007–08. He subsequently made the Stars' 2007–08 NHL roster out of training camp.
Professional
Dallas Stars
Niskanen made his NHL regular season debut against the Colorado Avalanche on October 3, 2007 to open the 2007–08 season. He recorded his first NHL points against the Boston Bruins two nights later with two assists. His first NHL goal came on October 29, 2007, against the San Jose Sharks. Niskanen had an excellent rookie start with the Stars, leading the team in plus/minus at mid-season, which resulted in his being invited to the Young Stars game during the 2008 NHL All-Star weekend.
Pittsburgh Penguins
On February 21, 2011, Niskanen was traded to the Pittsburgh Penguins in exchange for defenseman Alex Goligoski. During the 2013–14 season, on March 4, 2014, Niskanen had his first multi-goal game with a two-goal effort in a 3–1 win over the Nashville Predators away at the Bridgestone Arena. In the final year of his contract with the Penguins and approaching free agency, Niskanen finished the season establishing new career highs in goals and assists for 46 points.
Washington Capitals
On July 1, 2014, Niskanen signed a seven-year, $40.25 million contract as a free agent with the Washington Capitals. In the 2017–18 season, Niskanen continued to play top-four pairing minutes with the Capitals, posting 7 goals and 29 points in 68 games. He recorded nine points and appeared in all 24 games of the playoffs while logged over 25 minutes of ice time to help the Washington Capitals claim their first Stanley Cup. Returning for his 12th season in the NHL in 2018–19, Niskanen contributed with 8 goals and 17 assists for 25 points in 80 regular season games for the Capitals. He posted 2 assists in 7 playoff games, unable to help the Capital defend the Cup in a first-round defeat to the Carolina Hurricanes.
Philadelphia Flyers
On June 14, 2019, with two-years still remaining on his contract, Niskanen was traded by the Capitals to the Philadelphia Flyers in exchange for defenceman Radko Gudas.
