Obesity in adolescents is associated with non-communicable risk factors and diseases like metabolic-associated fatty liver disease (MAFLD), which is the liver manifestation of metabolic syndrome. L-citrulline is a non-protein amino acid that has shown positive effects on the degree of steatosis in animals with non-alcoholic fatty liver disease (NAFLD). The aim of the study was to evaluate the effect of oral L-citrulline supplementation on liver function and cardiovascular risk factors in adolescents with abdominal obesity and MAFLD. A prospective, double-blind clinical trial in adolescents with abdominal obesity was randomized into two groups: forty-two adolescents were supplemented with L-citrulline (6 g of L-citrulline/day) (n = 22) and placebo (n = 20) for eight weeks. The variables evaluated were anthropometry, blood pressure, glucose, insulin, HOMA-IR, L-citrulline, L-arginine, malondialdehyde, lipid profile, liver profile, urea, uric acid, and hepatic steatosis by ultrasound. After supplementation, the L-citrulline group had a decrease in liver fat accumulation (p = 0.0007); increases in body weight (p = 0.02), glucose (p = 0.03), and HOMA-IR (p = 0.03); and decreases in BMI (p = 0.002), total cholesterol (p = 0.001), HDL-C (p = 0.01), LDL-C (p = 0.002), and alkaline phosphatase (p = 0.05). L-citrulline for eight weeks decreases hepatic fat accumulation and LDL-C levels in adolescents with abdominal obesity and MAFLD.