In January 2013, after finishing his formation, Aguilar moved to fellow Categoría Primera A side Alianza Petrolera on loan.[4] He made his professional debut on 16 February, starting in a 4–0 away loss against his parent club.[5]
Aguilar scored his first professional goal on 10 April 2013, his team's third in a 4–0 away rout of Cúcuta Deportivo, for the national cup. He then became a regular starter at Alianza before returning to Nacional in January 2016.[6] Initially a backup to Alexis Henríquez and Davinson Sánchez, he became a regular starter after Sánchez's departure to Ajax.
Santos
On 15 January 2019, Atlético Nacional announced that they had accepted an offer from Santos for Aguilar.[7] Three days later, he was officially announced as the club's second signing of the season, after agreeing to a four-year contract.[8]
Initially a first-choice, Aguilar was demoted to fourth-choice in September 2019 (behind Gustavo Henrique, Lucas Veríssimo and new signing Luan Peres), mainly due to individual errors.[10]
Athletico Paranaense
On 18 March 2020, Aguilar agreed to a four-year contract with fellow top tier side Athletico Paranaense,[11] for a rumoured fee of R$ 10 million for 50% of his federative rights.[12]
In June 2021, Aguilar returned to Colombia to join Atlético Nacional on a one-year loan, with an option to join them permanently.[13]
On 1 July 2022, Aguilar joined Argentine Primera División club Lanús on a one-year loan.[14] In August 2023, he switched sides and joined Independiente on a 1.5 year loan, after his parent club indicated that he was not part of their plans for the current season.[15]
Aguilar made his full international debut on 11 June 2016, starting in a 3–2 loss against Costa Rica at the NRG Stadium in Houston.[18] In that year, he also represented the under-23s, being initially named for the 2016 Summer Olympics but being cut from the final squad due to injury.[19]