Rafael came to Grêmio in 2006, as an amateur player. In 2007, he captained the Under-20 side and featured in the Sendai Cup for the Brazil Under-18 national team in the same year but was an unused substitute in the tournament. He was promoted to the first team after captaining the youth side in the Copa São Paulo de Futebol Júnior by the coach Vágner Mancini, but soon was relegated to the youth squad because of his lack of commitment in pre-season training. Before the beginning of the 2008 Brazilian Serie A, Mancini was fired and Rafael earned a new chance from the coach Celso Roth, the same coach who promoted Ronaldinho to the first team in 1998. He became the team's first-choice in the central midfield and created a strong partnership with William Magrão. Appearing as a defensive midfielder, Rafael missed just one league match and received just five yellow cards during the season.