The Computer Science Doctoral Program begins with research and breadth components. The research component helps students place an early focus on research. Students must complete an "Introduction to Graduate Studies" course (CS 7001) and then take at least three credit hours of directed research study (CS 8903) under faculty guidance each semester until their qualifying examination. The breadth component is intended to facilitate students' learning about a variety of areas within computing, as well as core computer science areas. Students must take at least twelve hours from the different areas of study within the College. The current twelve areas are computer architecture, database systems, graphics and visualization, human-computer interaction, information security, intelligent systems and robotics, learning sciences and technology, networking and communications, programming languages and compilers, software methodology and engineering, systems (including operating systems, distributed and parallel systems), and theoretical computer science. Students must include courses from the systems and theory areas in those breadth courses.

As students' research progresses, they must select a primary, and possibly secondary, area of focus from the areas listed previously, and then pass a qualifier (comprehensive exam) in that area or areas. The qualifier consists of three parts:

1. A one-day written examination covering the pertinent research area(s)
2. The submission of a high-quality research deliverable, as evidenced by a portfolio consisting of at least an exam committee-reviewed and publishable article, and possibly other work products as approved by the exam committee
3. An oral presentation and examination

After successfully completing the qualifier, a student focuses on research leading toward a dissertation. The topic of the student's research is formalized through a written dissertation proposal followed by an oral presentation. When the student passes their proposal, the student is admitted to candidacy and proceeds with dissertation research. This phase is completed with the successful defense and submission of the approved doctoral dissertation. Students are also required to complete a six-hour minor outside the College.

All PhD programs must incorporate a standard set of Requirements for the Doctoral Degree.