Before moving to Switzerland, he played for PCC San José of the local league, called Asociación Rosarina de Fútbol in the Primera División B in Argentina. He also played in the youth of Lanús and Tiro Federal.
On May 18, 2010, it was announced that Zárate was signed by Red Bull Salzburg. On July 13, Zárate scored his first goal in his first match for Red Bull Salzburg. The goal was in the Champions-League qualifying match versus HB Torshaven.