Students may choose a thesis or nonthesis option leading to the MS degree. The thesis option requirements are a minimum of 9 quarter-courses plus at least 3 units of research that result in the oral defense of a satisfactory thesis. Four of the courses must meet distribution requirements in chemical engineering. Most students who finish their education with an MS degree typically complete the thesis option in 18 to 24 months and are eligible for financial aid from the department. The nonthesis option requires a minimum of 12 courses with the same distribution requirements as for the thesis option. Students who follow the nonthesis option normally complete their studies in 9 to 15 months and are not eligible for financial aid from the department.

In addition to a traditional masters degree in the Department of Chemical and Biological Engineering, McCormick offers a number of professional masters degree programs, including the Masters in Biotechnology, directed by William M. Miller.