As a coach, he led several Czech and Slovak clubs, including a Czech First League record of five seasons in charge of FC Viktoria Plzeň, whom he led to two league titles, one cup title, and three consecutive seasons of participation in the UEFA Europa League knockout stage – a record for any Czech club.

[5] In 2010, he led Viktoria Plzeň to the victory in the Czech Cup for the first time in the club history.

In October 2013 Vrba led Plzen for a 152nd consecutive top-flight match, setting a league record.

[8] His last game in charge of the club was the 2013–14 UEFA Champions League group stage tie against CSKA Moscow which Plzeň won 2–1 with a last-minute goal from Tomáš Wágner, thus earning them a place in the Europa League knockout stage.

At the end of the match, the fans unfurled a banner reading "always remember that it wasn't wasted time".