His parents, having embraced the principles of the Reformation, emigrated from Bruges to the Electorate of the Palatinate in 1578, in order to enjoy freedom to profess their new faith, and they sent their son to be educated at Strasbourg under Johann Sturm.

Crossing to England towards the end of 1582, he attended the lectures of John Rainolds (1549–1607) at Oxford, and those of William Whitaker at Cambridge.

Gomarus immediately set himself earnestly to oppose these beliefs in his classes at college, and was supported by Johann B. Bogermann (1570–1637), who afterwards became professor of theology at Franeker.

Gomarus took this defeat badly, resigned his post, and went to Middelburg in 1611, where he became preacher at the Reformed church, and taught theology and Hebrew in the newly founded Illustre Schule.

After his death, the Lyra Davidis was published, in which he sought to explain the meter of Biblical Hebrew poetry, and which created some controversy at the time, having been opposed by Louis Cappel.