Internal conflicts are inherent in organisations, including universities with more complex structures that specifically handle different functions in teaching and research. It is evident there are challenges of internal conflict in universities. This research therefore examined internal conflicts management strategies in Gombe State University and Federal University of Kashere. The objectives include to find out the most common types of internal conflicts in Gombe State University and Federal University of Kashere and to examined the most frequent factors responsible for internal conflicts in Gombe State University and Federal University of Kashere. The theory used for the study is Pluralist. The study employed questionnaire to collect data. The target population of the study are academic and non-teaching staff in the study area. 1,065 samples were selected using Krejcie and Morgan sample size calculator from the target population. From 1,065 distributed, only 1000 were duly filled and returned. The data collected were analyzed using simple frequency tables and percentages with the aid SPSS version 16. The findings show that the types of internal conflicts experienced in the two universities include; conflict between university management and academic staff unions and non-academic unions and conflict between academic staff unions and non-academic staff union among others. The study also found that most frequent factors responsible for internal conflict in the study universities include imposition of decision on employees by the university managements, refusal of the university managements to honor agreements reached with workers unions, competition over Tetfund conference/workshops and study fellowships among others. The study concluded that internal conflicts are inevitable in human life and so are they in institutions of higher learning including Gombe State University and Federal University of Kashere. Based on the findings, the study recommended the need for improved consultations, the need to adhere strictly to the guidelines for selection and nominations of staff for tetfund sponsorship and improved guidelines for sharing of earned academic allowances among academic and non-academic staff in the universities.