Intravesical therapy is widely used in non-muscle-invasive bladder cancer (NMIBC) as adjuvant treatment after transurethral resection of bladder tumor (TURBT). Assuming that adjuvant therapy is necessary for NMIBC in order to reduce recurrence and progression rates, chemotherapy and BCG toxicity become a relevant issue. Both treatments may have local and systemic side effects, which can lead to treatment cessation, resulting in incomplete treatment and poor outcomes. Therefore, urologists, specialist nurses and patients must be aware of the possible adverse events in order to early recognize, prevent and treat them properly. This article summarizes the local and systemic side effects associated with intravesical therapy, presents the recommendations for an effective management of these adverse events based on currently available evidence, and highlights some open questions on these issues.