During his playing career, Prusek appeared in 57 games in the National Hockey League (NHL) with the Ottawa Senators and Columbus Blue Jackets.

Martin Prusek started his professional ice hockey career in 1994 when he joined HC Vitkovice of the Czech Extraliga.

[2] After spending most of the 2005–06 season with the Blue Jackets AHL affiliate Syracuse Crunch, Prusek left North America and joined SKA Saint Petersburg in the Russian Super League.

In 2008-09 Prusek played in Kontinental Hockey League and after a brief contract with HC Spartak Moscow, he joined Dinamo Riga for 2 seasons.

In summer 2011, he stepped into HC Vítkovice Steel pre-season players' camp, but on July 26 he announced his retirement decision and also he accepted the club's offer for the position of goaltender coach.