Metabolic dysfunction-associated liver disease is related to impairment in glucose metabolism and amino acid metabolism in the liver and alpha-cell function, a feedback loop recently termed as the liver-alpha cell axis. We investigated the effect of liver fat content (LFC) in comparison to hepatic insulin resistance (HOMA-IR) on the liver-alpha cell axis in 84 normoglycemic children and adolescents (40 females, 44 males, 14.1±2.3 years) with varying degrees of obesity (BMI 33.5±5.0 kg/m², BMI-SDS 2.94±0.50). Patients were stratified according to LFC into metabolic dysfunction-associated liver disease (MASLD) (>5% LFC), non-MASLD (<5% LFC) groups and LFC quartiles. LFC was 10.08±10.30%, HOMA-IR 5.52±3.80 mmol/L, fasting glucose 5.08±0.73 mmol/L and glucagon 11.99±6.53 pmol/L. LFC correlated with glucagon and HOMA-IR (r=0.30, p=0.001; r=0.39, p<0.001, adjusted for age, sex and BMI-SDS). Of all amino acids analyzed, only branched chain amino acids (BCAA) correlated with glucagon (valine r=0.40 vs. isoleucine r=0.36 vs. leucine r=0.36, p<0.05) and HOMA-IR (valine r=0.43 vs. isoleucine r=0.39 vs. leucine r=0.35, p<0.05). In linear regression models, glucagon correlated with valine (R2= 0.10, p=0.002), isoleucine (R2=0.07, p=0.01) and leucine (R2=0.04, p=0.03), adjusted for age, sex and BMI-SDS. The significant association of all BCAA with LFC in the multiple regression models was lost when HOMA-IR, sex, age and BMI-SDS were added. In mediation analysis, the proportion of total effect of LFC on BCAA was highest in leucine (3.2% vs. isoleucine 1.9% vs. valine 2.1%, adjusted for age, sex and BMI-SDS). In comparison, the proportion of total effect of HOMA-IR showed more robust associations (valine 56.3%, isoleucine 57.7%, leucine 65.3%, adjusted for age, sex and BMI-SDS). In conclusion, plasma concentrations of BCAAs correlate with fasting glucagon and hepatic insulin resistance, independent of LFC in youth with obesity. Hepatic insulin resistance may be more important than hepatic lipid accumulation in modifying the effect of glucagon on amino acid turnover.