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This study is an empirical study that examined the challenges facing postgraduate students’ use of Electronic Information Resources [EIRs] for research output in federal university libraries in the southeast, Nigeria. It employed a descriptive survey design. The population of the study was registered postgraduate students in five universities libraries in 2017/2018 academic year comprising of 1,522 users. Yaro Yamane formula was used in calculating the sample size for each stratum in order to have proportional representation. A sample size of 421 postgraduate students was selected and used for the study. Instrument for data collection was questionnaire constructed on a four-point rating scale. Data collected were organised in tables using Statistical Package for Social Science (SPSS). Any item with a mean score response of 2.50 and above was accepted as an influencing factor. The result revealed that the challenges facing postgraduate students’ use of electronic resources for research output include; plagiarism, time consuming/waste of time, inadequate network computers, frequent breakdown of system, insufficient bandwidth, irrelevant information and lack of co-operation from library staff among others. While the identified strategies for enhancing the use of university libraries EIRs for research output by these postgraduate students include; proper orientation on EIRs usage, provision of relevant information, adequate training on information technology usage, provision of network computers; constant power supply and enhanced internet connectivity among others. Based on the findings, the study recommends that awareness should be created on the availability of these resources to PG students, increase budget allocation to libraries, training and re-training of all PG students during their first year in Nigerian universities on the use of EIRs for research; provision of alternative power supply such generators, solar energy systems and payment of subscription fees as at when due by library management.