The Florida Marlins selected Aguila as a third baseman in the third round of the 1997 MLB draft out of McQueen High School in Reno, Nevada; he had set a single-season home run record while at McQueen. Although he was initially a highly regarded prospect, he spent two seasons playing rookie ball in the Gulf Coast League and 2½ more seasons in Single-A before he was promoted to the Double-A Portland Sea Dogs. He became an outfielder during the 1999 season, when he played for the Kane County Cougars. When he started playing for Portland in 2001, he was in his fifth professional season, but was still only 22 years old. He batted .257 in 64 games with Portland. He returned to the Sea Dogs in 2002 and posted a .294 average. The Marlins switched their Double-A affiliation to the Carolina Mudcats the following year, and Aguila spent 2003 with the Mudcats, posting a .320 batting average in 93 games. It was then that Aguila once again showed his potential as a hitter, and the Marlins would invite him to their spring training in 2004.

Although Aguila did not make the Marlins' opening day roster in 2004, he impressed Marlins manager Jack McKeon, and he batted .312 for Triple-A Albuquerque. He had two stints in the Majors in 2004, paving the way for him to make the Marlins' opening day roster in 2005.

In 2005, Aguila was named the Marlins' fifth outfielder (behind Miguel Cabrera, Juan Pierre, Juan Encarnación, and Jeff Conine), but was used mainly in a pinch-hitting role. He logged only 16 at bats in the first two months of the season, and he was sent back to Albuquerque on May 27. While in Albuquerque, he regained his everyday role as the team's center fielder. He batted .351 with 7 home runs and 25 RBI in 35 games with Albuquerque, and he was promoted back to the Major Leagues on July 7, when the Marlins placed Josh Willingham on the disabled list. He spent the rest of the season in the Major Leagues, mainly as a pinch hitter; he started only 12 games all year, most of them while Encarnación was injured. He finished the 2005 season with a .244 batting average, no home runs, and 4 RBI in 78 at bats. Following the 2005 season, he played for Gigantes del Cibao in the Dominican Winter League.

Instead of remaining with the Marlins, he signed a minor league contract with the Pittsburgh Pirates on December 10, 2006, with an invitation to spring training. He joined the Pirates in spring training as a non-roster invitee, but did not make the team out of camp; and played for their Triple-A club, the Indianapolis Indians, where he hit (.250/.291/.360/651 in 172 at bats).

Aguila was signed by the New York Mets in March 2008, and he was assigned to their Triple-A team, New Orleans Zephyrs. On June 11, Aguila was called up from Triple-A New Orleans to the Major League team to replace Abraham Núñez who was designated for assignment, but he too was designated for assignment after appearing in only three games. On July 11 Aguila was again designated for assignment, and on July 15 he was sent outright to the minors.

He rejoined the Marlins organization as a free agent on August 26, 2010. In 2011 and 2012, he played for the New Orleans Zephyrs in the Marlins system.

He signed with Fortitudo Baseball Bologna of the Italian Baseball League in 2013.