He was born at Ghent, where his father Jacques de Waele had moved from Brussels, after the execution of Lamoral, Count of Egmont in 1568.
Walaeus was educated at Middelburg school, where he was taught by Jacobus Gruterus and Murdisonius, and then at the University of Leiden, under Franciscus Junius, Lucas Trelcatius, and Franciscus Gomarus.