Immediately after retiring, Bílek began coaching, precisely with Teplice. After a brief stint in Costa Rica, he returned home, going on to manage FK Chmel Blšany, FC Viktoria Plzeň and MFK Ružomberok. In 2006, he took charge of Sparta, replacing Stanislav Griga. He went on to win the Gambrinus liga in his first year and finish second in the following. He resigned from his position at Sparta in May 2008.