Boonen is a surname. Notable people with the surname include:
Arnold Boonen (1669–1729), Dutch painter Jacobus Boonen (1573–1655), Belgian bishop Jan Boonen (born 1940), Belgian racing cyclist Jorge Boonen (1858–1921), Chilean military officer Indy Boonen (born 1999), Belgian footballer Tom Boonen (born 1980), Belgian road bicycle racer