Castillo began his career with the Defensor Sporting youth team and made his Uruguayan Primera División debut in the 1999 season. He was loaned to Huracán Buceo in 2001. However, he soon moved on to Peñarol and made his debut in 2006. After a good spell with Peñarol, two years later in 2008, he joined to Brazilian Série A side Botafogo. In December 2009, he was released of the club and then he moved to Colombian side Deportivo Cali, in where he remained one season, winning the 2010 Copa Colombia. In the next season, he abandoned the club for high costs and then signed a one–season deal with Colo-Colo for play the national tournament and the 2011 Copa Libertadores. However, he had a very regular season and was sacked of the club in December. On 16 February 2012, he joined to Liverpool de Montevideo in the transfer deadline day of the South American football.