Writing a research paper as a graduation requisite by university students is an important part of university education. It is not a simple task for most university students who face several problems during writing the graduation project. Several kinds of research have been conducted onrecognising the challenges and problems that face students in academic writing, but to the researcher's best knowledge, no study has been conducted on the problems faced in writing a graduate research paper by Jordanian undergraduate students of the English Language and Literature major. Therefore, the present study aimed to investigate the academic writing challenges and difficulties encountered in writing graduation papers by EFL undergraduate students in the Department of English at Alzaytoonah University of Jordan (ZUJ). The data for the study was collected through distributing a questionnaire of three parameters: attitude about writing a research paper, methodology challenges, and background knowledge about research. The questionnaire is based on identifying the causes of the students' challenges in writing their graduation papers. The respondents were 45 undergraduate students of the English Language and Literature. The findings revealed that the most important problems were lack of an academic prerequisite of teaching the techniques of how to write a research paper, lack of knowledge of research paper writing process, lack of resources, lack of the methodology, etc. Thus, for these reasons, the present study attempts to present suggestions and recommendations to overcome such hurdles faced by graduate students in writing their graduation research papers.