Objective: To explore the application effect of flipped classroom combined with case-based learning teaching methods in pharmacoeconomics teaching. Methods: The students majoring in clinical pharmacy in 2019 were selected as the study subjects, and the cost-effectiveness analysis of different dosage forms of Yinzhihuang in the treatment of neonatal jaundice was selected as the teaching case. The flipped classroom combined with case-based learning teaching method was used to carry out theoretical teaching to the students. After the course, questionnaires were distributed through the Sojump platform to evaluate the teaching effect. Results: The results of the questionnaire showed that 85.71% of the students believed that the flipped classroom combined with case-based learning teaching method was helpful in mobilizing the learning enthusiasm and initiative, and improving the comprehensive application ability of the knowledge of pharmacoeconomics. 92.86% of the students think that it is conducive to the understanding and memorization of learning content, as well as the cultivation of teamwork, communication, etc. Conclusion: Flipped classroom combined with case-based learning teaching method can improve students’ knowledge mastery, thinking skills, and practical application skills, as well as optimize and improve teachers’ teaching levels.