Paul Aguilar began his career with Pachuca Club de Fútbol in 2002. He started off in Pachuca's affiliate (second division) team, Pachuca Juniors. In 2004, he was loaned to Indios de Ciudad Juárez for two seasons in order to gain more experience. After returning to Pachuca in 2005 and making 27 appearances with the "B team" (Pachuca Juniors), Aguilar made his first-team debut in the 2006 Apertura tournament on 6 August in a match against Cruz Azul, with the match ending in a 2–3 defeat. Paul Aguilar played the entire ninety minutes and scored a goal in the 56th minute of the game. Pachuca won the 2007 Clausura championship after defeating América in the final. Paul Aguilar became a mainstay within the squad and won the confidence of manager Enrique Meza. Aguilar would barely miss a game since earning a starting position at right-back during the 2008 Clausura. Paul Aguilar also participated in the 2008 and 2010 FIFA Club World Cups with Pachuca. His performance with the club earned him a spot in the final 23-man national team squad who would play the 2010 FIFA World Cup. After five years and ten seasons with Pachuca, Paul Aguilar was sold to América for the 2011 Apertura in exchange for Juan Carlos Silva and Enrique Esqueda.