This study investigated library instruction methods, effect and the challenges in academic libraries using the Federal University of Petroleum Resources Effurun (FUPRE) students as the target population. Library instruction is a core activity of academic libraries that entails educating, enlightening, guiding and helping the library users to identify, understand and utilize library information resources effectively. A survey research design was adopted for the study. The population is consisted of seven hundred and seventy-three 100 level students who registered for Use of Library (GSE 112) course in the first semester of 2015/2016 academic session. Questionnaire was the instrument used for data collection. Using a consensus sampling technique, all the 773 students participated in the study during a seminar organized for the 100 level students at the end of the second semester by August 2016. All the questionnaires were retrieved while 643 were found usable representing 83 percent. The finding showed that classroom teaching, library orientation and library guide (X = 3.00, SD = 000) were the methods mostly used while guided library tour (X = 2.53, SD = 667), and one-on-one mentoring (X = 2.48, SD = 716) were also used to instruct the library users. The study reveals that Ask a librarian, FAQ, library Blog, library Website, Text messaging were not used to instruct the users. It shows that library instruction is effective for identification of books on the shelves (X = 3.78, SD = 416), accessing and retrieving of information materials in the library (X = 3.67, SD = 471), enabling students to cite and reference books with ease (X = 3.11, SD = 874) and turning users into regular library users (X = 3.45, SD = 497). The study, however, showed that library instruction has no effect on students’ academic excellence (X = 3.44, SD = 687). The challenges facing library instruction including non-expository of the program (X = 2.78, SD = 785), inadequate time for library orientation (X = 3.00, SD = 815), non-utilization of information and communication technology (ICT) for library instruction (X = 2.78, SD = 787) and students’ lack of interest in library instruction programmes (X = 3.56, SD = 684) were identified. The study concluded that library instruction is an effective means of educating users and creating awareness of available information resources in the library. Therefore, librarians should ensure that library instruction impact students’ academic excellence while viable methods of engaging and instructing the users such as Ask a librarian, FAQ, library Blog, library Website, Text messaging should be explored.