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.
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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