Penn Ph.D. students in allied fields of study can also apply to enter the masters program in applied mathematics and computational science, which can allow them to earn both degrees simultaneously. Like other students in the AMCS masters program, students pursuing a secondary masters must also take at least eight graduate courses from the list of approved courses numbered 500 and above, including at least one each in applied algebra, applied analysis, probability and statistics, and numerical methods, or as appropriate given a student's primary field of study. With permission of the Graduate Group Chair, certain courses with a 400-number may be counted toward the course requirement for the Masters degree. The other courses can be in pure mathematics, applied mathematics, and courses offered by other departments, which make essential usage of advanced mathematics. Every student's program of study must be approved by the graduate group chair. Certain 500-level courses (e.g. MATH 502, 503, 508, 509), will only be approved for PhD students at Penn in other fields who are pursuing an AMCS Masters degree along the way.

There is also a requirement to pass the Written Preliminary Exam and to submit and defend a Masters thesis, or take two additional courses in lieu of the Masters thesis. To receive the Masters degree a student must have at least a 3.0 cumulative grade point average in AMCS related courses. Interested students should consult the main Masters Degree web-page, and contact the AMCS graduate group Chair.