A two-year long-term workshop centered around a phenotypic whole-cell screening strategy for integrating cutting-edge knowledge and discovery-based laboratory experiences was developed to serve as a preparatory course for enhancing the teaching quality of the upper-level discovery-based research internship curriculum for pharmacy major undergraduates. The workshop comprises four modules that integrate lessons and experiments into a genuine research project, which initiates with a medicinal-chemistry course, run concurrently in the second year and culminates with the discovery-based research internship curriculum for pharmacy major students as a corequisite in the last year. The effective implementation of the featured pedagogical approaches in the modules is detailed as described. A group of students (N = 4) passed the instructor-student two-way choice and were enrolled in the senior-level phenotypic hit discovery laboratory project. The students synthesized a small library of molecules, tested them in an antibacterial assay, and further designed new compounds to analyze structure-activity relationships. Furthermore, positive feedback from students revealed that the phenotypic hit discovery oriented workshop enabled them to gain in-depth cutting-edge knowledge and provided an understanding of how medicinal chemists engage in new drug discovery research. The student's early exposure to troubleshooting or exploring unexpected results in an authentic scientific environment inspired them with ambition and confidence to engage with new drug discovery. We hope that this workshop will serve as a springboard for those wishing to educate medicinal chemists at an undergraduate level with modern strategies that are relevant to the current and future drug discovery landscape.