Mentoring which is a process of tutoring a junior person in a workplace by a senior colleague is becoming more challenging especially in the university system. The objective of this study therefore is to provide empirical investigation in the Nigerian context on the challenges associated with mentoring for both the mentor and the protégé in the university system. The study employed a survey research design. The population consists of all academic staff in three randomly selected universities in Edo state namely: University of Benin, Ambrose Ali University, and Igbinedion University. The research instrument used was a structured questionnaire administered to academics across different cadres. Data collected were analyzed using frequency, percentages, mean, standard deviation, exploratory factor analysis, t-test and analysis of variance (ANOVA). All statistical analyses were done using Statistical Package for the Social Sciences (SPSS 24). The study found that prominent mentoring challenges among Nigerian university academics include victimization, instant gratification, gender-based bias, work life imbalance and incivility. It was also found that mentoring challenges experienced by academics do not significantly differ based on demographic characteristics such as status, gender, age, qualification and work experience. The study recommends that universities and other tertiary institutions should promote an atmosphere of organizational harmony where faculty members will seek the growth of younger academic staff for the advancement of the educational system.