It is rare for students to enter the PhD program at the University of Illinois after finishing this degree. Students may choose one of three tracks: Optimization and Algorithms, Applications to the Sciences, Computational Science and Engineering. This degree program requires 32 credit hours and can normally be completed in 18 months. A master's thesis is optional.

For the Applications to the Sciences and Computational Science & Engineering options, it is strongly recommended that the entering student has taken at least one course in each of linear algebra, real analysis, probability or statistics, and differential equations and has training in computer programming.