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.

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.

On 8 March 2017, during the Copa MX round-of-16 match against Tijuana, Aguilar headbutted referee Fernando Hernández.

As of 3 June 2015, Aguilar has played in 22 games with the Paraguay national team, scoring four times.