This study is intended to explore challenges in writing master theses from postgraduate English as Foreign Language (EFL) students' and supervisors' perspectives. To do so, 40 EFL postgraduate students and 10 supervisors were selected nonrandomly based on availability sampling from five major Iranian universities. Qualitative data were gathered via semistructured interviews the results of which were analyzed by utilizing thematic analysis. The findings revealed a number of main challenges faced by postgraduate students in writing master theses as reported by supervisors and the students themselves, some of which were common challenges for both groups. The main common challenge reported by both the students and supervisors was the students' lack of research knowledge including the inability to write academically using academic vocabularies, lack of research design knowledge such as analyzing data by SPSS software and choosing a researchable topic. Implications of the study for universities, EFL postgraduate students, and their supervisors are discussed in this study.