Levofloxacin is a synthetic fluoroquinolone that is usually used to treat chronic bacterial prostatitis. We investigated the safety and efficacy of levofloxacin compared with ciprofloxacin for the treatment of chronic bacterial prostatitis in Chinese patients. This was a multicenter, open-label, randomized controlled non-inferiority trial. Four hundred and seventy-one patients with clinical symptoms/signs were enrolled into the study, and 408 patients were microbiologically confirmed chronic bacterial prostatitis, who were randomized to either oral levofloxacin (500 mg q.d.) or ciprofloxacin (500 mg b.i.d.) for 4 weeks. Bacterial clearance rate, clinical symptoms/signs, adverse reactions and disease recurrence were assessed. The clinical symptoms and signs (including dysuria, perineal discomfort or pain) and bacteria cultures in 209 patients treated with levofloxacin and 199 patients treated with ciprofloxacin were similar. The most common bacteria were Escherichia coli and Staphylococcus aureus. One to four weeks after the end of 4 weeks treatment, the bacterial clearance rate (86.06% vs. 60.03%; P<0.05) and the clinical efficacy (including clinical cure and clinical improvement(93.30% vs. 71.86%; P<0.05)) were significantly higher in the levofloxacin-treated group than in the ciprofloxacin-treated group. The microbiological recurrence rate was significantly lower in the levofloxacin-treated group than in the ciprofloxacin-treated group (4.00% vs. 19.25%; P<0.05). Rates of adverse events and treatment-related adverse events were slightly lower in the levofloxacin-treated group than in ciprofloxacin-treated group. Levofloxacin showed some advantages over ciprofloxacin in terms of clinical efficacy and disease recurrence, with a low rate of adverse events, for the treatment of chronic bacterial prostatitis in Chinese patients.