"El Vasco" Arruabarrena (The Basque) 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 six months.

While with Boca, Rodolfo Arruabarrena won the Apertura in 1998 and the Clausura in 1999 Argentine first division tournaments, as well as the Copa Libertadores 2000.

He holds Villarreal's record of appearances in La Liga, with 178 first division matches with El Submarino Amarillo (as of 9 December 2005).

With Villarreal CF he won the UEFA Intertoto Cup in 2003 and 2004, and played 200 league and international matches for the Spanish team (as of 10 September 2006).

On 29 July 2008, AEK Athens manager Giorgos Donis announced to the press that Arruabarrena was no longer in the team's plans.