Born in Bilbao, Spain on 20 November 1965, Aretxaga has dual Spanish and Mexican citizenship;[2] her first name and paternal surname are Basque.[3] Her mother was a dressmaker and her father taught in an occupational school; she was part of the first generation of her family with a university education.[4]
She was an undergraduate at the Complutense University of Madrid, graduating with a bachelor's degree in physics in 1988.[2] She moved to the Autonomous University of Madrid for graduate study in physics, earning a master's degree in 1990 and completing her PhD in 1993.[2] Her doctoral dissertation, Variabilidad óptica de núcleos galácticos activos generados por formación estelar [Optical variability of active galactic nuclei generated by star formation was supervised by Ángeles Isabel Díaz Beltrán [es].[5]