Although fluoroquinolones are first-line agents for the treatment of National Institutes of Health (NIH) category II chronic bacterial prostatitis (CBP), therapy with these agents is not always feasible due to the increasing worldwide resistance of causative uropathogens. New therapeutic options are urgently required, as drugs such as β-lactam antibiotics distribute poorly to prostatic sites of infection and trimethoprim therapy is often unfeasible due to high resistance rates. The present study aimed to analyze the efficacy of aminoglycosides, administered to a cohort of 78 patients affected by fluoroquinolone-resistant CBP, or excluded from fluoroquinolone therapy due to various contraindications. Patients received netilmicin (4.5 mg/kg, once-daily, intramuscular), combined or not with a β-lactam antibiotic, for 4 weeks. Follow-up visits were scheduled 6 and 12 months after the end of treatment. Fifty-five out of 70 patients (78.6%) showed eradication of the causative pathogen, and a significant reduction of the NIH-Chronic Prostatitis Symptom Index (NIH-CPSI) total score from a baseline median value of 21 to 14 at the end of therapy, and to 9 and 8 at 6-month and 12-month follow-up assessments, respectively. The pain, voiding and quality of life subdomains of the NIH-CPSI decreased accordingly. In 15 patients showing persistence of infection, NIH-CPSI total and subdomain scores did not decrease at the end of therapy. Additional clinical parameters, such as the urinary peak flow rate, percentage voided bladder, serum prostate-specific antigen concentration, International Prostate Symptom Score and prostate volume improved significantly only in the group of patients in which the infection was eradicated. Therapy was well tolerated, and genetic testing for deafness-predisposing mitochondrial mutations allowed safer administration of aminoglycosides. These results suggest that aminoglycosides may become a therapeutic alternative for the treatment of CBP. These findings should be further validated in a randomized-controlled setting.