Authorities say 64-year-old Walter Lee Williams was arrested in the southern resort city of Playa del Carmen.
Williams was wanted on charges of sexual exploitation of children and traveling abroad for the purpose of engaging in sexual acts with children.
The indictment alleges Williams traveled from Los Angeles to the Philippines in January 2011 to engage in sex acts with two 14-year-old boys he met online in 2010, the U.S. Department of Justice said in a statement Monday.
Williams was a professor of gender and sexuality studies at USC until 2011. It was not immediately known when he will be extradited to Southern California.
The Associated Press contributed to this report.