ObjectivesExcellent anticancer effect for solid tumors with microsatellite instability (MSI)‐high by anti‐PD‐1 antibody has been reported. In this study, we investigated the clinical impact of MSI status in bladder cancer.MethodsThis study included 205 Japanese patients who underwent transurethral resection for bladder cancer between 2005 and 2021. The prevalence rates of microsatellite stable (MSS), MSI‐low (MSI‐L), and MSI‐high (MSI‐H) were determined using molecular testing. We examined the association of MSI status (MSS versus MSI‐L/H) with clinicopathological characteristics and oncological outcomes.ResultsMSI‐L/H tumors were associated with higher T‐category in non‐muscle invasive bladder cancer (NMIBC). Additionally, MSI‐L/H tumors were associated with a higher risk of intravesical recurrence in NMIBC patients treated with intravesical bacillus Calmette‐Guérin (BCG) but not with non‐BCG therapy.ConclusionsThis study suggested that the MSI status might serve as a predictive marker for intravesical recurrence after BCG intravesical therapy in NMIBC and highlighted an unmet need for an alternative treatment in patients with MSI‐L/H tumors.