Problem based learning (PBL) is a teaching methodology that gives precise indications to guide students of Physiology towards the analysis of situations and problem solving. In this project, 120 second year undergraduate pharmacy students were divided in groups of 12 students each. They were exposed to PBL activities led by facilitators. Real situations related to the Physiology of the digestive system as a case-problem were presented in the UCM Virtual Campus. Students were provided with clear guidelines for aims and objectives of the debate and related questions for the development of the practice sessions. One week later, on the day of the debate, students analyzed the clinical problems, formulated hypothesis, and undertook self-directed learning tasks. In addition, the PhysioEX 9.0 software allowed students to use a simulated virtual laboratory where they assessed the activity and enzymatic function as a replica of actual case-problem. Also, a histological study of the different areas of the digestive system such as stomach, small and large intestine, salivary glands, pancreas and liver were also carried out. Pre and post-test were conducted for knowledge assessment. At the end of the week, the students completed a questionnaire regarding their PBL experience and on the suitability of each of the different materials used, as well as the attitudes generated by the implementation of the PBL system in the Physiology practical teaching. The obtained results indicated that the incorporation of PBL as a learning strategy in the physiology practices sessions had a positive impact on learning. The use of simulation coupled to PBL improved the acquisition of critical assessment and management skills, increased the interest and involvement of students in their own learning, encouraged participation among work teams, generated a critical thinking of greater clarity for the acquisition of new competences and allowed feedback of learning (self-evaluation). Thus, the student will deepen the practical physiological mechanisms that are the basis of their knowledge as future pharmacists, which will allow them to propose effective therapeutic strategies. All this PBL experience will help to better understand an integrating vision of the functioning of the digestive system.