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We identified 8 pediatric patients on micafungin (MCFG;≥ 3 doses) at our institution who had breakthrough candidemia (BC). The causative strains of the BC were Candida parapsilosis in 7 patients. The minimum inhibitory concentration of MCFG was≤ 1 µg/mL (susceptible) in all 8 isolates. Immunocompromised patients may develop BC caused by MCFG-susceptible strains.