Urinary tract infections (UTIs) are a common condition in children and often lead to hospitalization. A considerable proportion of children with UTIs (up to 30%) experience at least one recurrence, placing them at risk for long-term complications such as renal scarring. Since the concept of the microbiome was first introduced in 2001, increasing attention has been given to the role of the urinary tract microbiome in maintaining urinary tract homeostasis. Dysbiosis of the urinary microbiome has been recognized as a factor associated with an increased risk of various urinary tract diseases, including UTIs. However, the specific role of the urinary microbiome in the pathophysiology of pediatric UTIs remains incompletely understood. The present review examines recent studies on the urinary microbiome in children and summarizes current strategies for modulating the urinary microbiome to prevent UTI recurrence in the pediatric population.