Chilavert appeared for the Paraguay national football team 74 times from 1989 to 2003, scoring 8 goals and representing the team at five major tournaments. Chilavert appeared for Paraguay at two FIFA World Cup tournaments (1998 and 2002), where he served as captain on both occasions, and appeared in three Copa América tournaments (1991, 1993, and 1997). Chilavert was also included in the 1998 FIFA World Cup Team of the Tournament.