Uncomplicated lower urinary tract infections (UTIs) are the most frequent infections in females. Increased resistance rates against commonly used antibiotics have led to the use of novel antimicrobials. The aim of the present study was to evaluate the bacteriological and clinical effects of single-dose fosfomycin trometamol (FMT) and 5-day ciprofloxacin in females with uncomplicated UTIs. In this randomized comparative study, 260 female patients between 18 and 65 years of age enrolled, of whom 142 completed the study. The most frequently isolated bacterial pathogen in the urine cultures of patients were Escherichia coli (82.3%) and Enterobacter spp. (8.4%). FMT sensitivity was 94% and ciprofloxacin sensitivity was 59% in Escherichia coli; in comparison, FMT sensitivity was 75% and ciprofloxacin sensitivity was 50% in Enterobacter spp. The MIC90 for FMT was 4 μg/ml. Of the 142 patients, 77 were treated with FMT and 65 were treated with ciprofloxacin. The clinical remission rate was 83% in the FMT group and 81% in the ciprofloxacin group; the bacterial eradication rate was 83% in the FMT group and 78% in the ciprofloxacin group, and there was no significant difference between the two study groups. In conclusion, a single dose of FMT (at 3 g) was as effective as ciprofloxacin, at 500 mg twice a day for 5 days, in the treatment of uncomplicated lower UTIs. It was concluded that the use of FMT as a first-line treatment in the empirical treatment of uncomplicated UTIs might have a positive impact on the problem of resistance to other antibiotics.