Background: Worldwide, microbes are becoming more challenging by acquiring virulent skills to adapt and develop antimicrobial resistance (AMR). This is a concern as AMR increases morbidity, mortality, and costs. Consequently, physicians need to be trained on appropriate antimicrobial prescribing, starting as medical students. Objective: To evaluate medical students’ confidence in antimicrobial prescribing and AMR. Methods: Cross-sectional study assessing medical students’ knowledge, perception, and confidence in prescribing antimicrobials and AMR in a Malaysian University. A universal sampling method was used. Results: Most responding students believed that educational input regarding overall prescribing was sufficient. Regarding the principle of appropriate and accurate prescriptions, female medical students had less knowledge (odds ratio (OR) = 0.51; 95% confidence interval (CI) 0.25–0.99; p = 0.050). Year-IV and Year-V medical students had more excellent knowledge than Year-III students regarding confidence in potential antibiotic prescribing once qualified. Year-V students also showed an appreciably higher confidence in the broad principles of prescribing, including antibiotics for infectious diseases, compared to those in other years. Conclusion: Overall, medical students gain more knowledge and confidence regarding the potential prescribing of antimicrobials as their academic careers progress. This is important given concerns with the current excessive use of antimicrobials in Malaysia.