The supervisory practices, particularly in undergraduate thesis writing, have not received sufficient attention, specifically regarding their impact on EFL students writing apprehension and the potential gender differences in these dynamics. To fulfil this gap, this study examines the path coefficients among supervisory problem dimensions (research interests, different expectations, limited support, personal relationships, personal conflicts), writing self-efficacy, academic writing competence, toward writing apprehension, focusing on the potential gender differences among EFL students. A Partial Least Square Structural Equation Modeling (PLS-SEM) analysis was performed on a total of 219 EFL students undertaking their undergraduate thesis writing. The study revealed supervisory problems through mediated variables of academic writing competence and writing self-efficacy influence writing apprehension (=0.214 and =0.509, respectively; p 0.000 for both). Furthermore, the multi-group analysis uncovered notable gender differences. In contrast with male students, in which only a few paths were statistically significant, all paths were found to be significant for female students. In particular, the path from supervisory problem to academic writing competence had the strongest impact on female students, indicating the heightened sensitivity to supervisory problems related to the students writing apprehension. These novel findings shed light on the gender difference impact on the academic writing process, and a more pronounced impact from supervisory problems on their writing apprehension frequently happened to female students. Accordingly, these findings highlight the importance of recognizing and addressing those differences in instructional strategies to promote a more encouraging and productive learning environment.