Brückner began his coaching career in 1973 with his home club SK Sigma Olomouc, before moving to FC Zbrojovka Brno, who he led in the Czechoslovak First League in the 1981–82 and 1982–83 seasons. He later went on to coach Inter Bratislava with which he won the Slovakia Cup in 1985.
Brückner became the national team manager in 2001, following the Czech Republic's unsuccessful qualifying campaign for the 2002 FIFA World Cup. In the time up to March 2004, the Czech Republic played twenty matches without defeat under his leadership, winning seven of eight qualifying matches for the Euro 2004 tournament and drawing the other one. In the tournament's group match against the Netherlands, the Czech Republic conceded two goals within the first 20 minutes. Although Jan Koller scored a goal to make the score 2–1, Brückner responded by taking the unusual step of making a tactical substitution during the first half of the match, sending on midfielder Vladimír Šmicer to replace defender Zdeněk Grygera after just 25 minutes. The Czech Republic scored twice more, with Šmicer scoring the winner two minutes before the end, as Brückner's team completed a comeback. The team went on to reach the semi-finals of UEFA Euro 2004.
The team qualified for the 2006 FIFA World Cup but did not progress past the group stage. Brückner extended his contract for a further two year period after the competition. The Czech Republic qualified for Euro 2008. Prior to the tournament, Brückner announced his intention to leave his position at the end of the competition. The Czech Republic failed to progress beyond the group stage of the tournament.