Abstract: The current study investigated third-year English-majored students’ perceptions towards the development of learning autonomy through implementing a fifteen-week project in one class. This research also aimed to explore the challenges students encountered in project-based learning. The data were collected by means of questionnaire and analyzed using descriptive statistics. The study results showed that students developed their learning autonomy in terms of independence but their study habits did not change much when project-based learning was implemented. In the meanwhile, learners also encountered undesirable challenges involving time, collaboration skills, presentation skills and lack of fundamental specialized knowledge and real-life experiences.