Poor health as a child meant that he was educated at home until age 13, but in 1912, after three years study at the gymnasium (high school), Pijper entered the Utrecht Academy of Music, where he was taught composition by Johan Wagenaar, passing examinations in theoretical subjects in 1915.
Pijper spent much of his time during the war years working on a new opera, Merlijn, based on the Arthurian legend.