He started performing as a conductor in 1914. Van Hoogstraten also conducted Brahms Festival in Vienna and Mozart Festival in Salzburg. In the twenties, Willem began his career in the United States. He led The New York Philharmonic Orchestra at the Lewisohn Stadium summer concert series from 1922 to 1939. In 1927, Van Hoogstraten conducted NYPhil playing Rhapsody in Blue and Concerto in F with George Gershwin as soloist.
In 1925, Van Hoogstraten was appointed a music director of the Oregon Symphony Orchestra where he served for thirteen seasons. He also worked as a permanent conductor of Das Mozarteum Orchester Salzburg from 1939 to 1945.