Novotný's first NHL point came in his second game, when he assisted on a Daniel Paille goal against the Los Angeles Kings on January 14, 2006.

He was traded on February 27, 2007 to the Washington Capitals with a 1st round pick in the 2007 NHL Entry Draft for Dainius Zubrus and Timo Helbling.

[1] At the conclusion of the season, he was not extended a qualifying offer by the Capitals, making him an unrestricted free agent.

[2] On July 2, 2014, he signed a two-year contract with Lokomotiv Yaroslavl, after Lev Praha announced not to participate in 2014–15 KHL season.

[3] Having returned to the Czech Republic to begin the 2018–19 season with HC Plzeň of the ELH, on September 20, 2018, one day prior to the start of the National League, Novotny was signed to a two-month contract worth CHF 500,000 by HC Ambrì-Piotta to replace injured Bryan Lerg.