In addition to a general Masters Degree, the Penn's Mathematics Graduate Program offers Masters degrees with concentrations in Applied and Computational Mathematics. The requirements are the same as the general Masters Degree except that the Masters Thesis and at least four of the courses taken for the Masters Degree must be designated as being in the concentration.

Courses given in the Mathematics Department or elsewhere in the university can be designated by the Graduate Group Chair as being in the applied and/or in the computational mathematics concentration. The following is a partial list of designated courses:

- Math 524/525 - Topics in Modern Applied Algebra
- Math 530 - Mathematics of Finance
- Math 546/547 - Probability, Stochastic Processes
- Math 570/571 - Introduction to Logic and Computability
- Math 574/575 - Mathematical Theory of Computation
- Math 580/581/678 - Combinatorial Analysis and Graph Theory
- Math 582/583 - Applied Mathematics and Computation
- Math 584/585 - The Mathematics of Medical Imaging and Measurement
- Math 590/591 - Advanced Applied Mathematics
- Math 594 - Advanced Methods in Applied Mathematics
- Math 644/645 - Partial Differential Equations
- Math 670/671 - Topics in Logic
- Math 676 - Advanced Geometric Methods in Computer Science
- Math 680/681 - Applied Linear Analysis
- Math 691 - Topics in Mathematical Foundation of Program Semantics
- Math 692/693 - Numerical Analysis
- Math 694/695 - Mathematical Foundations of Theoretical Physics