The effectiveness of quinolone prophylaxis in high-risk hematological pediatric patients is controversial. A systematic review was performed according to PRISMA guidelines, including studies that involved children and young adults undergoing chemotherapy for acute leukemia or HSCT and that received quinolone prophylaxis compared to no prophylaxis. Meta-analysis was performed on blood-stream infections and neutropenic fever. Data regarding the impact of prophylaxis on overall survival, antibiotic exposure, antibiotic-related adverse effects, antibiotic resistance, Clostridium difficile infections, fungal infections, length of hospitalization, and costs were reviewed in the descriptive analysis. Sixteen studies were included in the qualitative analysis and ten of them met the criteria for quantitative analysis. Quinolone prophylaxis resulted effective in reducing the rate of blood-stream infections and neutropenic fever in pediatric acute leukemia compared to no prophylaxis, but it had not a significant effect in HSCT recipients. Prophylaxis was associated with a higher rate of bacterial resistance to fluoroquinolones, and higher antibiotic exposure.