This empirical work studied the use of institutional repositories in Nigerian university libraries. Three specific objectives and research questions were formulated to guide the study which was the extent of use of institutional repositories by staff in the two university libraries; the problems affecting the use of institutional repositories in the university libraries; and the strategies for improving on the challenges of using institutional repositories in the two Nigerian university libraries. A descriptive survey research design was adopted for the study. Out of 5000 thousand population of the study, 300 staff was selected using stratified and multi-stage sampling techniques. A structured questionnaire was used for gathering data and the data gathered was analyzed using mean, tables, and frequency counts. From the findings, it was discovered that the most used or accessed materials in the institutional repositories by staff are journaled articles, theses and dissertations, books, faculty and departmental journals, and book chapters. These among others are some of the problems of using institutional repositories by staff in the two university libraries. It (institutional repositories) has not been user-friendly, there is also inadequate training to researchers on how to use the repository, power outage, members of the academic community are not properly sensitized on the institutional repositories. It was recommended that there is a need to make the institutional repositories user friendly by using familiar keywords and metadata while developing their contents and that librarian should market the institutional repository contents to staff and other researchers so as to know what they have to access and use them for their studies and research.