In October 2007, Paul Aguilar received his first call-up by coach Hugo Sánchez to play a friendly match against Nigeria, however he did no see playing time.
In 2009, Aguilar was called-up again, this time by coach Javier Aguirre, and made his debut with the national team on 30 September in a friendly match against Colombia.
The match ended in a 1–2 defeat, with Aguilar played the entire 90 minutes and scoring Mexico's only goal.

In early 2010, Aguirre called-up Aguilar for a series of international friendlies in preparation for the 2010 FIFA World Cup.
Mexico's first game of 2010 was a 5–0 win over Bolivia, in which Paul scored his second goal for Mexico in only his second appearance.
He eventually made the final 23-player roster for the World Cup.

He started in the tournament's inaugural match against hosts South Africa, but was substituted out for Andrés Guardado in the 55th minute.
He did not participate in any of the next three matches.

Aguilar was a part of the winning squad at the 2011 CONCACAF Gold Cup, however he only saw playing time in the semi-final match against Honduras.
Aguilar also participated in the 2011 Copa America held in Argentina, playing in all three group matches as a right-back.
In 2012, he saw no activity with the national team.

Aguilar would not receive another call-up until late 2013, this time by new coach Miguel Herrera for the two World Cup intercontinental playoff matches against New Zealand.
Aguilar would go on to score Mexico's first goal in the 5–1 win over New Zealand at the Estadio Azteca on 13 November.
The playoff ended in a combined 9-3 win for Mexico, thus qualifying them to the 2014 FIFA World Cup.
Aguilar would be included in the final 23-man squad for the World Cup.
During the 2014 World Cup, he started at right-back for Mexico in all four matches.

During the 2015 CONCACAF Cup, a one-off tournament meant to serve a qualifier to the 2017 FIFA Confederations Cup, Aguilar scored a game-winning volley in overtime for Mexico in the 3–2 result.

In the run-up to the 2018 FIFA World Cup, national coach Juan Carlos Osorio decided not to call-up Aguilar following alleged criticism from the player towards Osorio’s tactics.
In October 2007, Paul Aguilar received his first call-up by coach Hugo Sánchez to play a friendly match against Nigeria, however he did no see playing time. In 2009, Aguilar was called-up again, this time by coach Javier Aguirre, and made his debut with the national team on 30 September in a friendly match against Colombia. The match ended in a 1–2 defeat, with Aguilar played the entire 90 minutes and scoring Mexico's only goal.
In early 2010, Aguirre called-up Aguilar for a series of international friendlies in preparation for the 2010 FIFA World Cup. Mexico's first game of 2010 was a 5–0 win over Bolivia, in which Paul scored his second goal for Mexico in only his second appearance. He eventually made the final 23-player roster for the World Cup.
He started in the tournament's inaugural match against hosts South Africa, but was substituted out for Andrés Guardado in the 55th minute. He did not participate in any of the next three matches. 
Aguilar was a part of the winning squad at the 2011 CONCACAF Gold Cup, however he only saw playing time in the semi-final match against Honduras. Aguilar also participated in the 2011 Copa America held in Argentina, playing in all three group matches as a right-back. In 2012, he saw no activity with the national team.
Aguilar would not receive another call-up until late 2013, this time by new coach Miguel Herrera for the two World Cup intercontinental playoff matches against New Zealand. Aguilar would go on to score Mexico's first goal in the 5–1 win over New Zealand at the Estadio Azteca on 13 November. The playoff ended in a combined 9-3 win for Mexico, thus qualifying them to the 2014 FIFA World Cup. Aguilar would be included in the final 23-man squad for the World Cup. During the 2014 World Cup, he started at right-back for Mexico in all four matches.
During the 2015 CONCACAF Cup, a one-off tournament meant to serve a qualifier to the 2017 FIFA Confederations Cup, Aguilar scored a game-winning volley in overtime for Mexico in the 3–2 result.
In the run-up to the 2018 FIFA World Cup, national coach Juan Carlos Osorio decided not to call-up Aguilar following alleged criticism from the player towards Osorio’s tactics.
Paul Aguilar