The Computer Science department offers a major consisting of 44 credits and a minor consisting of 23 credits. Both the major and minor have Teacher Certification tracks. The department also has a emphasis in Computer Engineering Technology in collaboration with Western Technical College in a 2+2 program. It also participates in a dual degree program where students can receive a CS BS from UW-La Crosse and an Engineering BS from UW-Madison.
Unique to the department is a dual degree option for completing both the Computer Science BS degree and the Master of Software Engineering (MSE) degree in a 5-year combined track.