Universities rely on endogenous inputs they have to enroll and train students to graduate. Studies have concluded that graduation rates are low at research masters and doctoral degree levels in universities. This study determined endogenous inputs uses which predict internal efficiency in postgraduate research degree programmes in two Ghanaian public universities. The study used data obtained from a sample of 318 research students and graduates from nine applied science and sixteen humanities departments. Stratified random and snowball sampling techniques were used to sample participants for the study. Questionnaires and documents analysis guides provided data to test hypothesis at p<. 05 alpha level of significance. Faculty and students’ interactions, use of study spaces, reading resources at departments and libraries are endogenous inputs uses which accounted for high levels of variation in graduation rates and significantly predicted research students’ graduation rates. The study recommended among others that policy should be crafted aimed at increasing endogenous inputs uses in universities to ensure higher internal efficiency thus high students’ graduation rates.