Beeckman was born in Middelburg. He studied literature and philosophy in Leiden and graduated in 1618 in medicine from Caen. After a short time working for his father's business, making candles and water conduits, he became an assistant rector in Utrecht and later in Rotterdam. In 1627 he became rector of the Latin school in Dordrecht. He died at the age of 48 in Dordrecht.
Beeckman was a student of Simon Stevin. He was a teacher to Johan de Witt and was friendly with René Descartes, who dedicated one of his first tractatus to him, the Compendium Musicae. Later in life they fell out over a dispute concerning whether Beeckman had helped Descartes with some of his mathematical discoveries. In his time, he was considered to be one of the most educated men in Europe.
Beeckman did not publish his ideas, but he had influenced many scientists of his time. Contemporaries mention his ideas. After his death, most of these accredited ideas could be read in his diary called Journaal. Rejecting Aristotle, Beeckman developed, independent of Sebastien Basson, the concept that matter is composed of atoms. Beeckman is mentioned to be one of the first persons describing inertia correctly, however he also assumes that a constant circular velocity is conserved. Furthermore, Beeckman had shown that the fundamental frequency of a vibrating string is proportional to the reciprocal of the length of the string. In the analysis of the functioning of a pump he theorized that air pressure is the cause and not the then popular theory of horror vacui.