Beeckman was born and raised in the city of Middelburg, capital of the Dutch province of Zeeland, where his father had established himself as a candlemaker. Owing to his father's difficulties with the Reformed Church in Middelburg, Isaac was sent to the Latin schools at nearby Arnemuiden and Veere, before entering Leiden University in 1607 to study theology and mathematics. The well-known Ramist mathematician and philosopher Rudolph Snellius (father of Willebrord Snellius) was one of his teachers. Beeckman left Leiden in 1610 but was unable to find a place as a minister in the Reformed Church and ended up practicing his father's trade in the city of Zierikzee (he also repaired water conduits in breweries and fountains). By 1616, however, he handed over his shop to his assistant and took up the study of medicine. In September 1618 he traveled to Caen in Normandy, where he received a doctorate in medicine on a thesis on intermittent fevers. After his return to the Dutch Republic, he entered upon a career as a schoolmaster in the Latin schools of Utrecht (1619–20), Rotterdam (1620–27), and finally Dordrecht, where he was rector of the school (1627–37).

During these years, Beeckman kept a scientific diary, the so-called Journael, in which he noted his highly remarkable and original insights into the workings of nature. Only a few friends were allowed to consult his notebooks, among them Descartes, whom Beeckman had met in November 1618, when the future philosopher had joined the Dutch army in the city of Breda. During the final months of 1618, the two of them became intimate friends and discussed mainly mathematical and physical problems. Descartes dedicated his first work, Compendium of Music to Beeckman, who influenced Descartes’ “physico-mathematical” theory of music. They lost contact after Descartes had moved on to Germany, but reestablished their friendship on Descartes’ return to the Netherlands in 1628. However, partly because of some misunderstanding caused by a remark of Marin Mersenne, Descartes and Beeckman soon fell out with each other. Descartes accused his former friend of claiming to be his master, whereas, Descartes asserted, he had learned nothing from Beeckman that was worth mentioning.