Padilla played in the 1989 Intercontinental Cup, going 0 for 2 for the champs. In the 1990 Baseball World Cup, Padilla was two for four with a double as the backup to Pacheco at second, Cuba taking Gold. In the 1991 Intercontinental Cup, Juan was Cuba's starters and hit .275/.333/.450 with 9 RBI in 11 games, tying Lazaro Junco for second on Cuba behind Luis Casanova. He tied for 4th in the event with two homers. He was named the tournament All-Star second baseman, beating out Japan's Koichi Oshima, who had better stats. He was 0 for 3 in the Gold Medal game and made an error but Cuba squeaked past Taiwan, 2-1.