The 49-year old former Flamengo, Vasco da Gama and Deportivo La Coruna striker said he was unable to devote the time necessary for the job.
Bebeto is currently one of the three members on the local organising committee for the 2014 World Cup that will be held in Brazil, as well as a state legislator in Rio de Janeiro.
He was appointed in late January after Brazil's U20 team was surprisingly knocked out of the South American championship with just one win in four games.
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At the time he declared he would overhaul the youth team set up but his appointment was treated with scepticism due to his lack of experience.
He coached just one club, America in Rio de Janeiro in 2010, and lasted just eight games in charge.
The popular striker is perhaps best known for his "rock the baby" celebration during the 1994 World Cup in the United States when Brazil won its fourth world title.
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