Peña gained a total of nine14 [[Cap (sport)|caps]] for three [[Spain national youth football team|Spanish youth teams]]. He helped the [[Spain national under-20 football team|under-20s]] finish second at the [[1985 FIFA World Youth Championship]] in the [[Soviet Union]], appearing in the group stage against [[Brazil national under-20 football team|Brazil]] (0–2 loss) and the [[Republic of Ireland national football team|Republic of Ireland]] (4–2 win).<ref>{{cite web|url=http://www.fifa.com/worldfootball/statisticsandrecords/players/player=193079/index.html|title=Manuel Peña|publisher=FIFA.com|date=|accessdate=18 November 2012}}</ref>