Objectives Undergraduate dentistry students in their final year often lack the knowledge and confidence required to prescribe oral health medications. Online courses could help to solve this problem through augmenting traditional teaching methods. This study assessed the effectiveness of a non‐curricular, online, clinical case‐based dental pharmacology course designed to improve medication management in senior dentistry students. Materials and methods This study developed and implemented an online dental pharmacotherapy course for 287 dentistry students in Mexico. Pre‐ and post‐course tests evaluated knowledge acquisition, and a 5‐point Likert scale questionnaire was administered to 238 participants to evaluate the course's content and educational strategies. Results Mean knowledge scores significantly increased from pre‐ (5.5 ± 1.6) to post‐test (9.1 ± 1.3, P < 0.001). Participants reported a high satisfaction level (70.2%) with the course content and materials, educational techniques, and instructors. Conclusion These findings support the use of online, clinically based dental pharmacotherapy courses, in conjunction with traditional teaching methods, as a viable strategy for effectively educating dentistry students.