The oldest part of the building opened in 1972, including the current old gym, library, and small auditorium.

Athletic teams include: Waunakee has had a long time rivalry with fellow Badger North Conference member the DeForest Norskies.

Kokopelli Kafe is run by Waunakee High School's students with special needs.

Kokopelli Kafe philosophy is reflected in the goal: “Kokopelli Kafe is a school based business that enables students to learn functional, transitional, vocational, and social skill in a “real life” environment.”[7] Waunakee Community High School offers clubs relating to construction, arts, chemicals, agriculture, sports, culture, business, and more.

Students in Pay it Forward participate in volunteer work and support local and distant communities.

[8] Waunakee's Fine Arts Department includes programs in band, orchestra, choir, and drama.

On March 17, 2022, multiple articles were released accusing Waunakee schools of allowing students to identify and even dress up as furries.