Isaac Aboab da Fonseca was born into the Aboab family in the Portuguese town of Castro Daire as Simão da Fonseca. His parents were Marranos, Jews who had been forcibly converted to Christianity. Although the family had ostensibly converted to Christianity, this did not put an end to local antisemitic suspicions. When Isaac was seven, the family moved to Amsterdam. From that moment on, the family "reconverted" back to Judaism, and Isaac was raised Jewish from that moment on. Together with Manasseh ben Israel, he was given lessons by the scholar Isaac Uziel.