Background/Objectives: While antibiotic prophylaxis is crucial for preventing infections, its impact on the development of antibiotic-resistant infections and clinical outcomes remains underexplored. We aimed to systematically assess the impact of medical and surgical antibiotic prophylaxis (SAP) on the development of antibiotic-resistant infections, clinical outcomes, and costs. Methods: A systematic review and meta-analysis of the effect of antibiotic prophylaxis on antibiotic-resistant infections, mortality, length of hospital stay, and/or costs was conducted in hemato-oncological or surgical patient populations. Pooled estimates of the relative risk (RR) or weighted mean difference (WMD) were derived using random-effect meta-analysis. Results: Of 10,409 screened studies, 109 (30%) comprising 131,519 patients were included. In 55 hemato-oncological studies, prophylaxis significantly reduced Gram-negative infections (RR: 0.51; 95% CI: 0.45 to 0.59) without an effect on mortality (RR = 1.01; 95% CI: 0.89 to 1.15), while the risk of developing an infection resistant to prophylactic antibiotics during hospitalization was doubled (RR: 2.05; 95% CI: 1.88 to 2.23). The length of hospitalization was reduced by 1.85 days. Among 54 surgical studies, SAP lowered surgical-site infections (RR: 0.58; 95% CI: 0.49 to 0.69). Extending prophylaxis beyond the recommended duration did not improve infection rates (RR: 1.10; 95% CI: 0.98 to 1.24). No association was demonstrated between prophylaxis adjusted by colonization status and the development of resistant infections. Conclusion: Though proven beneficial, our results highlight the critical need for targeted antibiotic stewardship programs (ASPs) in both settings. A meticulous risk assessment balancing the benefits of preventing life-threatening infections against the risk of driving antimicrobial resistance, and a tailored ASP, is urgently needed for hemato-oncological patients.