In 2002, after failing to break into the first team at Bohemians, he moved to Czech Second Division side FK Mladá Boleslav.

Bednář finished the 2003–04 season as top scorer with 10 goals as Mladá Boleslav won the Second Division title.

On 27 July 2005, Hearts announced that they had completed the signing of Bednář on a one-year loan deal from FBK Kaunas.

He made his return on 26 November against Motherwell in a 1–1 draw,[6] and played his part in Hearts' successful second-place finish and Scottish Cup victory.

Bednář started the 2006–07 Scottish Premier League season in a rich vein of form, scoring three times, twice in the 2–1 victory over Celtic at Tynecastle.

[16][17] Bednář signed a three-year contract, with Albion paying Hearts £2.3 million for the player, in addition to the £200,000 loan fee they had paid previously.

On 17 October 2009, Bednář suffered a back injury (a trapped nerve) in the early stages of Albion's game against Reading.

[26][27] He made his debut three days later, as a late substitute against Coventry City, setting up former Baggies teammate Kevin Phillips for an 87th-minute equalizer in a 2–1 win at Bloomfield Road.