We aimed to characterize the urinary microbiome of catheterizing patients with neurogenic lower urinary tract dysfunction (NLUTD) and to evaluate differences based on type of bladder management or frequency of urinary tract infections. This is a prospective, cross-sectional study of urine samples from asymptomatic, catheterizing patients with neurogenic lower urinary tract dysfunction who used either clean intermittent catheterization or indwelling catheters. Patients without symptoms of urinary tract infection provided a catheterized urine sample for urinalysis, culture and bacterial community microbiome analysis. A total of 95 patients submitted urine for analysis, of whom 69 had sufficient sequence reads (>1,203) for microbiome analysis. Cases with low bacterial signal amplification were associated with use of vaginal estrogen, no intradetrusor botulinum toxin A use and no growth on standard urine culture. The most abundant operational taxonomic units were from the phylum Proteobacteria, classified as Enterobacteriaceae and Escherichia. Alpha diversity varied among those who used indwelling catheters vs clean intermittent catheterization, and those who underwent botulinum toxin A injection vs not. On linear discriminate analysis, the relative abundance of the operational taxonomic units identified as Pseudomonas was higher among patients using indwelling catheters relative to clean intermittent catheterization. The operational taxonomic unit identified as Aerococcus was at a higher relative abundance among males compared to females. Enterobacteriaceae and Escherichia were the most abundant genera in the urinary microbiome of patients with neurogenic lower urinary tract dysfunction. Urinary microbiome diversity varied based on bladder management type. Future clinical correlations between microbiome of neurogenic patients and clinical presentation may help guide treatment strategies.