A complete central midfielder with good tackling, technique, and offensive qualities, together with accurate passing and goalscoring ability,[2][3] he played mostly for Valencia during a 17-year professional career, being an essential figure in five of the club's major titles, which included two La Liga championships.

[4] Baraja was also a consistent part of the Spain national team for five years, appearing in one World Cup and one European Championship and winning 43 caps.

[6] When Atlético was relegated at the end of 1999–2000, Baraja left the club in a 2,000 million pesetas transfer to that year's UEFA Champions League finalists Valencia,[7] who were looking to strengthen their central midfield following the sale of first-team players Gerard and Javier Farinós.

Baraja closed his chapter at the Mestalla Stadium after one full decade on 16 May 2010, receiving homages before and after the 1–0 home win over Tenerife and being replaced to a standing ovation in the 89th minute.

[27] On 22 December 2013, Baraja took interim charge of the reserves in the Segunda División B, as Nico Estévez was doing the same for the first team, and achieved a 2–1 win at Sant Andreu.

[34] Towards the end of the season, he received a four-match ban and a €3,005 fine for preventing Barcelona B's Sergi Palencia from taking a throw-in;[35] this included the first game of the play-offs, in which eventual champions Valladolid eliminated the Asturians 5–2 on aggregate in the semi-finals.

[36] On 18 November 2018, Baraja was dismissed after losing the Asturian derby against Real Oviedo, leaving the team in 14th position with a streak of only one win from 11 matches.