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