Purpose: Diagnosing urinary tract infections by urine culture is time-consuming during a Bacillus Calmette-Guérin treatment. Because the urine culture results take time to collect, patients are treated presumptively, or Bacillus Calmette-Guérin is discontinued before the results. This study evaluated the ability of the Sysmex UF-1000i system to examine the urine bacterial count and determine if it could be used to predict a positive culture. Materials and Methods: 180 patients who underwent transurethral resection for bladder tumors and received intravesical Bacillus Calmette-Guérin treatment between January 2017 and July 2018 were evaluated prospectively. For patients who received an intravesical Bacillus Calmette-Guérin treatment, urine flow cytometry, and urine cultures were assessed weekly during the treatment period. Results: During Bacillus Calmette-Guérin instillation, 44, 146, and 27 patients had bacteriuria, pyuria, and positive urine nitrite, respectively. Multivariate analysis indicated that the predictors associated with bacteriuria included the urine flow cytometry results of >100 bacteria/l (odds ratio, 22.73; p<0.001) and positive urine nitrite (odds ratio, 5.67; p=0.012) at the time of sampling for positive urine culture. The area under the receiver operative characteristic curve for diagnosing bacteriuria by urine flow cytometry was 0.825. A urine flow cytometry cutoff value of >100 bacteria/l resulted in a sensitivity and specificity of 75% and 90.91%, respectively. Using the cutoff of >1,000 bacteria/l, the sensitivity and specificity were 50% and 94.85%, respectively. Conclusions: Rapid urinary tract infection diagnosis using Sysmex UF-1000i can be used to determine whether to treat an infection and to avoid unnecessary Bacillus Calmette-Guérin discontinuation and urine culture tests.