Problem Based Learning (PBL) is a learning method for students who focus on a problem in learning. PBL method prepares students to have critical and analytical thinking based on the appropriate learning resource. Before doing the learning, students’ learning motivation is strongly needed in completing the learning process. The implementation of PBL method in Medical and Health Science Faculty of University Muhammadiyah Yogyakarta included giving learning to the students in the form of expert lecture, tutorial, lab work, skill lab, plenary discussion, interprofessional education (IPE) and e-learning. This study aimed to find out the impact of PBL on students learning motivation of Medical and Health Science Faculty of Yogyakarta Muhammadiyah University. This reaserch is non-experimental descriptive by cross sectional approach. This reaserch was conducted on October 2016-August 2017. The data collecting technique used simple random sampling by giving questionnaire to the students. The total of respondent was 222 students. It consisted of 80 students of Doctor students batch 2014, 47 students of Dentistry students batch 2014, 55 students of Nursing Study Program batch 2013 and 40 students of Pharmacy students batch 2014. The results of the study indicate that there is an impact of PBL on the students learning motivation of Medical and Health Science Faculty of University Muhammadiyah Yogyakarta by 34%. The percentage indicates that PBL gives good impact on the students learning motivation of Medical and Health Science Faculty of University Muhammadiyah Yogyakarta.