He played one season for HC Vítkovice of the Czech Extraliga before joining the Whalers' American Hockey League (AHL) affiliate, the Springfield Falcons, in 1994–95.

Marek scored his first career NHL goal on October 19, 1996, against Jeff Reese and the New Jersey Devils in a 6–2 Whalers victory.

The following season, his ninth with the Whalers/Hurricanes franchise, Malík was traded to the Vancouver Canucks along with Darren Langdon in exchange for Jan Hlaváč and Harold Druken.

He completed his second season with the Canucks, in 2003–04, as co-recipient of the NHL Plus/Minus Award (shared with Martin St. Louis of the Tampa Bay Lightning) with a +35 rating.

On November 26, 2005, Malík scored on Washington Capitals netminder Olaf Kölzig to finish the then longest shootout in NHL history.

[citation needed] During his time with New York, Malík was criticized for his lack of physical play, despite his size, as well as his risky decision-making with the puck.