Waunakee Community High School has numerous student organizations. Of note:
Other clubs include:
KEEP Energy Educator Awards: The Wisconsin K-12 Energy Education Program (KEEP) annually sponsors the Energy Educator of the Year Award to increase the visibility of the network of outstanding educators across the state of Wisconsin. The 2014 winners included Betsy Buckley of Waunakee Community High School.
The district received Wisconsin Environmental Education Board grants for a solar project and integrating fuel cell technology.