Problem Based Learning (PBL) is a learning method that involves students to solve problems by step-step in scientific approach. So, the students not only can study the knowledge related to the problem but also solve the problem. PBL become one of learning approach that apply the problems in a context for students to practice how to think critically and integrated all of their knowledge. Since its established in 2010, undergraduate education program Pharmacy Department Muhammadiyah University of Yogyakarta using PBL learning method. The importance of measuring the level of knowledge and students perceptions of PBL method to determine what aspects need to be developed and evaluated so as to provide a picture of how the knowledge and perception of Pharmacy students UMY for PBL learning method. This study is descriptive analytic by cross sectional approach, using quota sampling as sampling method. A total of 105 respondents from first year Pharmacy UMY student (2014 class) until fourth year Pharmacy UMY student (2011 class) using 25 items questionnaire include 12 items to measure of knowledge and 13 items to measure the level of knowledge and perceptions of Pharmacy students UMY against PBL learning method. Measurements score of respondents using a Likert scale with the categories of knowledge and perception as follows: Good 76% -100%, enough 56% -75%, Less Good 40% - 55%, and No Good <40%. The results showed that the level of knowledge of Pharmacy students UMY for PBL learning methods that are in good category (98.41%), while the perception of the students were in either category (83.88%). The conclusion of this study is the level of knowledge and perceptions of Pharmacy students on the PBL is good.