Background: Institutions may have different interpretations of Problem-Based Learning (PBL) characteristics. As a result, the implementation of PBL may be completely different from one institution to another. Aim: This study aims to evaluate and compare the implementation of PBL at the Faculty of Medicine, Suez Canal University (FOM-SCU), Egypt, and Ibn Sina National College for Medical Studies (ISNC), Saudi Arabia from the viewpoint of the student at both schools. Methods: This is a descriptive study, conducted at the FOM-SCU and ISNC and a convenience sample was taken from students in both schools (381 students at FOM-SCU and 479 students at ISNC). A validated, self-administered questionnaire was used to evaluate the quality of PBL implementation from the students' points of view. Validity and reliability studies have been done for the questionnaire after its translation into Arabic. Descriptive statistics together with regression analysis were applied, using SPSS v.20. Results: Overall students' satisfaction with the current implementation of PBL gave mean scores of 3.44±0.70 and 3.59 ±0.63 at ISNC and FOM-SCU, respectively. Scores were consistently higher for FOM-SCU students over all the evaluated subscales. Statistically significant differences (p < 0.05) in student-centered learning, self-directed learning, and the quality of the small groups have been found between both schools, consistently higher in FOM-SCU. Conclusion: The current study found that students are moderately satisfied by the quality of PBL at their respective schools. However, moderate scores indicate that there is room for more improvement in the implementation of PBL at both schools, especially in the training of PBL facilitators. Students at FOM-SCU were more satisfied by PBL at their schools than students of ISNC, especially regarding student-centered learning, self-directed learning, and the quality of the small groups.