Aguilar won the Paraguayan Primera División title with his first club, Sportivo Luqueño, in 2007. He then transferred to Argentine Primera División side Colón de Santa Fe, where he played for one year. Subsequently, Aguilar played for San Luis of the Mexican Primera División, before joining Argentine Primera’s side Arsenal de Sarandí.

In 2012, Aguilar was sent on loan to Club Tijuana. He started in 20 matches for the club during the Apertura tournament, which Tijuana won, defeating Toluca in the final, even scoring one of the goals himself.

As of 3 June 2015, Aguilar has played in 22 games with the Paraguay national team, scoring four times. He scored his first goal on 17 October 2012 in the 1–0 victory against Peru.

On 18 December 2013, it was announced that Aguilar was transferred to Club América, with the announcement being made on the club’s Twitter account. On 8 March 2017, during the Copa MX round-of-16 match against Tijuana, Aguilar headbutted referee Fernando Hernández. Despite initially being given a ten-game suspension, a strike by the referee’s association protesting the punishments of Aguilar and Enrique Triverio of Toluca ultimately led to a revised year-long ban for Aguilar from any official football activity. On 31 March, it was reported that both Aguilar and Triverio would appeal their bans to the Court of Arbitration for Sport.

In 2015, Aguilar became a naturalized Mexican citizen.

In the summer of 2018, Aguilar officially became a player for Cruz Azul. On 21 July 2018, Aguilar debuted in a 3–0 victory against Puebla and played the 90 minutes.