Following his career as a player, Krejčí became coach of Příbram reserve football team.
Krejčí joined Czech First League side Plzeň as manager in April 2008 for the end of the 2007–08 Czech First League after Levý´s departure. In new season he became assistant of new head coach Jaroslav Šilhavý and later Pavel Vrba. This coach duo Vrba-Krejčí started in Plzeň very successful era, in which the club won two league titles, one cup title, and three consecutive seasons of participation in the UEFA Europa League knockout stage. When in December 2013 Vrba joined the Czech Republic national football team as head coach, Krejčí continued to work with him as his first assistant.
In August 2015, Krejčí was named as the new manager of Viktoria Plzeň after Miroslav Koubek´s departure because of unsuccessful start of new season.