His career was connected especially with Sigma Olomouc, Viktoria Plzeň and Hertha BSC.

In January 2007, FC Moscow signed Hubník from SK Sigma Olomouc for a €2 million transfer fee.

[1] On 20 May 2010, Hertha made use of a contract option and signed Hubník permanently.

On 5 July 2009, Hubník made his debut for the Czech Republic national team in the match against Malta.

At the European championship in 2016 in France, Hubník played in all three group-stage matches for the Czech national team.