Gamarra appeared for the Paraguay national team 110 times, scoring 12 goals, from 1993 to 2006, representing the team at 10 major tournaments and captained the squad during the latter part of his career. He is the second most capped player of the national team, his record being broken by Paulo da Silva in 2013. Gamarra appeared for Paraguay at three FIFA World Cup tournaments (1998, 2002 and 2006), five Copa América tournaments (1993, 1995, 1997, 1999 and 2004), and twice at the Summer Olympic Games (1992 and 2004, with Paraguay claiming Silver Medals in the latter). Gamarra was named as the Paraguayan Footballer of the Year in 1997 and 1998, and was also included in the 1998 FIFA World Cup Team of the Tournament.