The 44-year-old replaces FA chairman Ivan Hasek, who quit as coach last week after Czech Republic failed to qualify for next year's World Cup.
"It is an offer you do not refuse," Bilek said after getting the nod from Hasek, his former team mate at Sparta Prague and for Czechoslovakia at the 1990 World Cup. He was also an assistant during Hasek's time as national coach.
Apart from Czech clubs, Bilek has coached teams in Slovakia and Costa Rica, and won the league and cup double with Sparta Prague in 2007.
The Czechs had been favourites in European qualifying Group Three to make it to South Africa next year but finished third behind Slovakia and Slovenia.
Bilek is the team's fourth coach in the past year. He will seek to lift a squad who have struggled to adjust to life without some of the key players who took the team to appearances at Euro 2004, the 2006 World Cup and Euro 2008.
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