In March/May 1996, Mendieta was part of the Spain under-21 team which was runner-up in the UEFA European Championship. He made his senior side debut on 27 March 1999, coming on as a substitute for Juan Carlos Valerón in a 9–0 thrashing of Austria for UEFA Euro 2000's qualifying stages; he was included in the list of 22 for the competition in Belgium and the Netherlands, helping the national side reach the last eight.