Nowak began playing professional soccer at the age of 15, when he debuted in 1979 for Włókniarz Pabianice in his native Poland, with whom he played his first four years. Nowak would go on to play for Zawisza Bydgoszcz, Motor Lublin, and Widzew Łódź before leaving Poland for Bakırköyspor of the Turkish first division in 1990. Nowak then played for Young Boys Berne of Switzerland and Dynamo Dresden before moving to the Bundesliga in 1994 by signing with FC Kaiserslautern. After that, Nowak moved to 1860 Munich, where he would play until 1998, and with whom he was voted the best playmaker of the Bundesliga for the 1995-96 season, as well as Polish player of the year in 1996. Nowak was also an important player for the Polish national team, which he captained for three years, and for whom he played 24 games and scored three goals.
In 1998, Nowak moved to the United States to play in Major League Soccer for the Chicago Fire. In their inaugural season, Nowak led the Fire to a victory in the MLS Cup, and was soon recognized as one of the best players in the league. He also led the Fire to two US Open Cup victories, playing 114 league games for the team, registering 26 goals and 48 assists. Nowak played with the Fire until 2002, when, due to salary cap constraints, he was traded to the New England Revolution, which immediately spurred his retirement. After a year off, Nowak was appointed as head coach of D.C. United starting in the 2004 season. He quickly pulled the team together and led D.C. to their fourth MLS Cup.
In 2003, Nowak was named the first member of the Ring of Fire, the highest honor the Chicago Fire will bestow upon a person; and his name and number 10 are displayed high at midfield at Toyota Park, their new stadium. In 2005, Nowak was named to the MLS All-Time Best XI.
On December 20, 2006, the Washington Post reported that Nowak would be leaving United to act as assistant to Bob Bradley with the United States Men's national team, and the Under-23 Men's national team, which will compete at the 2008 Beijing Olympics.