Learner autonomy, an educational goal which is highly related to higher education, is almost taken for granted among scholars and educationalists though its fulfillment helps learners take charge of their learning needs. Nevertheless, what is actually achieved in all probability is not the desirable goal line designated in terms of developing learner autonomy in EFL settings. Given these considerations among university students in higher education, the present study addressed the perceptions of students of Shiraz University of Applied Science and Technology on learner autonomy in academic EFL courses. To this end, semi-structured interviews were conducted. The data were thematically analyzed in accordance with the principles of qualitative data analysis that is the content-analysis of the data. Remarkably, facilitating and impeding factors to learner autonomy were found in EFL classes based on what the participants mentioned. The students’ conception of learning was based on the principles of learning in learner autonomy. They conceived their role as what was in line with the students’ role in autonomous learning. There was not a considerable distinction among male and female students regarding what they indicated about their conception of learning, their role in the learning process and their views toward different aspects of learner autonomy in EFL courses. Subsequently, it was highly recommended that there should be more attention to the principles of learner autonomy as well as learners’ needs and interests to create a more stimulating environment to motivate the students to become self-motivated and active participants in the process of learning in EFL educational contexts.