Recent research in language learning and teaching has prompted revived attention to developing learners’ critical thinking skills. Training learners to think critically serves as a significant opportunity to improve their knowledge and skills, yet it is still a key issue in need of enormous research in terms of its application. Despite its evident importance, the way to enhance students’ thinking skills is challenging and impeded by numerous barriers. This survey study sets out learners’ perceived barriers to critical thinking in two state Moroccan universities. Surveying 110 EFL students, the respondents were invited to openly comment on the obstacles that hindered their reflection. By way of qualitative content analysis, the results displayed that enhancing critical thinking skills is governed by factors related to teaching, learning and the education system. Amongst the nine challenges the Moroccan students face, lecturing and student content knowledge were reported to be the two major obstacles that significantly influenced the development of critical thinking.