According to the problems that pharmacy students face in their education system, this study is trying to find a solution to improve motivation and learning skills in students. The pharmacotherapy course was restructured according to the learner-centered approach. Team working, finding solutions for different cases and challenges and sharing it with class, is the main idea of this study. The Motivated Strategies for Learning Questionnaire (MSLQ) was administered to students before and after taking the course, and changes in MSLQ subscales from baseline were evaluated. Compared to baseline, students’ intrinsic goal, self-efficacy, critical thinking, and metacognitive self-regulation was improved after taking the course. Students responded positively to the learner-centered approach. Additionally, students with a clinical practice career orientation or who were prepared frequently for classes could achieve higher score on several MSLQ domains. So according to the results we can admit that the learner-centered approach and team working were effective in promoting several domains of motivation and learning strategies in a third-year pharmacotherapy course.