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To date, there is only one published report of an outbreak of urinary tract infections by <i>Salmonella</i> species after cystoscopy. Disinfection procedures for cystoscope have come into question. The current study aimed to determine the odds of developing <i>Salmonella</i> bacteriuria after cystoscopy. A retrospective case-control study was conducted on all patients with <i>Salmonella</i> species in urine (case) and blood (control) from 2017 to 2019 in 16 hospitals in Eastern Ontario, Canada. Eight of the 11 patients had cystoscopy prior to <i>Salmonella</i> bacteriuria; three of the 74 patients had urological procedures prior to <i>Salmonella</i> bacteremia, but none of their procedures were cystoscopy. The odds ratio of urological procedures with <i>Salmonella</i> bacteriuria was 63.1 (95% CI 10.9 to 366.6; <i>p</i> < 0.0001). In the bacteriuria group, the most frequently identified isolates were <i>Salmonella enteritidis</i> (n = 8), followed by <i>Salmonella oranienburg</i>, and <i>Salmonella heidelberg</i>. Seven of the <i>S. enteritidis</i> isolates had identical susceptibilities (ampicillin-sensitive; sulfamethoxazole/trimethoprim-sensitive; ciprofloxacin intermediate). In the bacteremia group, the most frequently identified isolates were <i>S. enteritidis</i> (n = 22), followed by <i>Salmonella typhi</i>, <i>S. heidelberg</i>, <i>S. oranienburg</i>, and <i>Salmonella typhimurium</i>. The result suggested cystoscopy is a risk factor for <i>Salmonella</i> bacteriuria. Identification of <i>Salmonella</i> bacteriuria should prompt public health investigations of linkage between cystoscopy and <i>Salmonella</i> bacteriuria.