After being selected by the Boston Bruins in the fourth round (No. 106) of the 2005 NHL Draft, Vladimir Sobotka played two mores seasons with Slavia Praha HC in the Czech Extraliga before signing an entry-level contract with the Bruins.

Sobotka spent time with Boston and Providence of the American Hockey League the following season. In 48 NHL games, he scored one goal and had six assists.

Sobotka again split time with Boston and Providence in 2008-09 before sticking with the Bruins in 2009-10, when he had 10 points (four goals, six assists) in 61 games.

After the season he was traded to the St. Louis Blues for David Warsofsky on June 26, 2010. Sobotka capitalized on his chance in St. Louis, getting 29 points (seven goals, 22 assists) in 65 games in his first season before signing a three-year contract extension with them on June 15, 2011.

Two seasons later, Sobotka set NHL career highs in assists (24) and points (33) in 61 games for St. Louis, but after his contract expired, he decided to play in Russia, where he spent the next three seasons for Omsk Avangard in the Kontinental Hockey League.

However, Sobotka returned to the NHL on April 7, 2017, when he signed a three-year contract with the Blues. Two days later, he scored a goal in his only regular-season game against the Colorado Avalanche before getting six points (two goals, four assists) in 11 Stanley Cup Playoff games.

In his first full NHL season in more than three years, Sobotka had 31 points (11 goals, 20 assists) in 81 games, but he was traded by St. Louis to the Buffalo Sabres as part of the package for forward Ryan O'Reilly on July 1, 2018.

In 2018-19, Sobotka had 13 points (five goals, eight assists).