The Academic Cell manages the CSIR-CCMB PhD Program, overseeing admissions, coursework, laboratory allotment, Doctoral Advisory Committee (DAC) meetings, Comprehensive Examinations, thesis submission, and maintenance of academic records and AcSIR documentation. Administrative matters for the JNU-CCMB PhD Program are handled separately by the JNU-CCMB Committee.

PhD admissions are conducted twice a year (January and August) through a written test and interviews. Since its inception, CSIR-CCMB has awarded 499 PhD degrees, preparing researchers with strong technical and analytical skills to address interdisciplinary scientific challenges.

During 2024–25, 18 students joined the program, bringing the total enrolment to 146 as of March 2025. In the same period, 13 students presented their PhD colloquia, 19 submitted their theses, and 24 were awarded PhD degrees under JNU/ACSIR.