Born in Río Cuarto, Córdoba, Aimar's football career begun in earnest when he was offered the chance to play for Estudiantes de Río Cuarto by youth coach Alfie Mercado. He trained with the club's academy three times a week and it was there that he was spotted by River Plate who offered the chance to join their own academy. Aimar's father initially prevented him from joining River as he felt he was too young to be playing football, but relented after manager Daniel Passarella personally asked him to allow his son to play. Having turned down the opportunity to attend medical school to pursue a career in football, Aimar made his debut for River on 11 August 1996 against Colón. His first goal for the club came on 20 February 1998 against Rosario Central. Aimar lifted five titles with River between 1996 and 2000, scoring 21 goals and recording 28 assists in 82 league appearances for the club, with his final appearance coming on 17 December 2000 in a 3–2 loss to Lanús.