The study examined the challenges facing students in the process of writing theses and identify differences in these challenges in light of gender, qualifications, mental status, career status, type of university. A survey descriptive design was employed as a questionnaire was a administrated to a random sample consisting of (438) master degree students. To achieve the study objectives, a questionnaire was used. The study showed that the level of challenges students face when writing thesis was moderate, and statistically significant differences in the level of challenges students face when writing thesis in light of gender, in favor of females; specialization, in favor of science; marital status, in favor of married; career status; in favor of employed, while there were no statistically significant differences in light of type of university. The main conclusions of the study is that material challenges were the most prevalent in the Jordanian universities. In light of the results, some recommendations were suggested.