Heereboord was born in Leiden, where he studied philosophy and theology at the university and, in 1640, was appointed reader in logic there. In 1642 he also became deputy dean of the Statencollege (a theological college for bursars of the States of Holland and Holland townships), the dean being Jacobus Revius (1586–1658), a very orthodox theologian, vehemently opposed to Cartesian philosophy. Heereboord's main task in the college was to train the students by organizing disputes on philosophical questions. From 1644 on he was ordinary (full) professor in philosophy. Heereboord did not have an easy life. The sordid details of his married life, mostly related to his drinking habits, were spelled out in several pamphlets by his brothers-in-law, Jan (1622–60) and Pieter de la Court (1618–85), also known as political theorists. The ecclesiastical authorities constantly intervened to prevent a permanent separation.

From the beginning of his professional career Heereboord was critical of Aristotelianism, by which he meant the slavish following of Aristotle. His own position was in all respects eclectic, also as far as modern philosophers were concerned. In fact, he believed that the method of philosophy consists in confronting different ideas instead of commenting on the works of a single author. This caused him to embrace Descartes’ work as a useful contribution to philosophy, barely a few weeks after having defended the notion of substantial forms against Regius (1598–1679). However, apart from the fact that he scrupulously avoided issues that could undermine orthodox reformed theology, what one finds in his works and disputations is a provocative defense of isolated ideas and propositions of Descartes (such as “cogito, ergo sum is the first certainty of philosophy” or “doubt is the beginning of a philosophy not subject to doubt”) rather than a systematic rethinking of the Cartesian project as a whole. On the other hand, he was one of the few Dutch Cartesians to tackle metaphysical problems, in defiance on the official ban on metaphysical teaching issued by the Leiden administration.