"El Vasco" Arruabarrena debuted professionally in 1993 with Boca Juniors, where he played until 2000, except for the Apertura 1996, when he was lent to Rosario Central for 6 months. After returning to Boca, he gained a place in the regular squad. Whilst with Boca, Rodolfo Arruabarrena won the Apertura in 1998 and the Clausurain 1999Argentine first division tournaments, as well as the Copa Libertadores 2000. He played a total of 178 games for Boca in all competitions, scoring 7 goals.
Villarreal
From Boca he moved to Spanish Villarreal in mid 2000. Because of his reliability while playing as the team's left-back, he has been the team's captain in several occasions. He holds Villarreal's record of appearances in La Liga, with 178 first division matches with El Submarino Amarillo. Arruabarrena's goals in the 2005–2006Champions League helped to eliminate Scottish giants Rangers FC and Italians Internazionale to reach the semi-finals in the club's first ever season in the competition. With Villarreal CF he won the UEFA Intertoto Cup in 2003 and 2004, and played 200 league and international matches for the Spanish team.
On 3 May 2007, El Vasco signed a three-year contract with Greek Super League runners-up AEK for 800,000 euros per year for two years, extendable for a third. According to Arruabarrena, an important role for his decision to continue his career in Greece was played by Lorenzo Serra Ferrer and Demis Nikolaidis. In Rivaldo's debut with AEK Arruabarrena set up the Brazilian legend to score on a header. Arruabarrena also set up Ismael Blanco to score against Getafe in a UEFA Cup match. Arruabarrena managed to have 25 appearances for AEK in one season but halfway through the season he suffered a serious injury. On 29 July 2008, AEK Athens manager Giorgos Donis announced to the press that Arruabarrena was no longer in the team's plans.
International career
El Vasco played 6 matches with the Argentina national football team, as well as several with the youth team. Arruabarrena made his first cap against Chile in 1994. He also played some matches in 1995 and one against England on 23 February 2000. Arruabarrena was not called up again for national team duty until September 2006, when Alfio Basile called him for a friendly match against Spain, and then again in February 2007 for another friendly against France. Arruabarrena was also called up for another friendly match against Chile on 18 April 2007 but he was left on the substitutes' bench.