Abdominal bioelectrical impedance analysis (aBIA) has been in use to measure visceral fat area (VFA) in adults. Accurately measuring visceral fat using aBIA in children is challenging. Forty-six school-aged Japanese children aged 6–17 years (25 boys and 21 girls) were included in this study. All were measured, and their VFA obtained using aBIA (VFA-aBIA) and abdominal computed tomography (CT) (VFA-CT) were compared. VFA-aBIA was corrected using the Passing–Bablok method (corrected VFA-aBIA). The relationships between corrected VFA-aBIA and obesity-related clinical factors were analyzed, including non-alcoholic fatty liver disease (NAFLD) and serum leptin and adiponectin levels. Boys had higher VFA-CT than girls (p = 0.042), although no significant differences were found in their waist circumference, waist-to-height ratio, and body mass index. The corrected VFA-aBIA using y = 9.600 + 0.3825x (boys) and y = 7.607 + 0.3661x (girls) correlated with VFA-CT in both boys and girls. The corrected VFA-aBIA in patients with NAFLD was higher than that in those without NAFLD. Serum leptin and adiponectin levels were positively and negatively correlated with corrected VFA-aBIA, respectively. In conclusion, corrected VFA-aBIA was clearly correlated with VFA-CT and was related to NAFLD and serum leptin and adiponectin levels in school-aged Japanese children.