Indonesian students have relatively poor learning autonomy. It is due to the fact that teachers explain material and solve example questions without involving students. This results in learners’ inactiveness and less learning autonomy. Therefore, there is a need to enhance students’ learning autonomy, one of which is by integrating Problem Based Learning (PBL).The goal of this study was to investigate the autonomy of students taught by implementing Problem Based Learning and students taught by applying conventional learning. This study was an experimental research with pre-test and post-test control group design. The population in this study was all grade VII students at SMP Negeri 3 Banda Aceh with which two classes were selected through random sampling technique. The instrument employed to obtain the data was students’ learning autonomy questionnaires. The statistical tests used in analyzing the questionnaires were t-test and two-way anava test to assess potential differences at all students’ levels. Based on the research, it was found that (1) Students’ learning autonomy toward mathematics when using Problem Based Learning (PBL) was better than students’ learning autonomy when using conventional learning, (2) There was no correlation between Problem Based Learning (PBL) and students’ levels (high, medium, low) toward students’ learning autonomy.