In this study, children with phenylketonuria and healthy control subjects were assessed for glutathione peroxidase (GSH-Px), superoxide dismutase (SOD), catalase (CAT) activity, malondialdehyde (MDA), glutathione (GSH), retinol, cholecalciferol, α-tocopherol, phylloquinone, total sialic acid (TSA), lipid bound sialic acid (LSA), total antioxidant (TAS), total oxidation (TOS), and amino acid levels, and the relationships of these variables with phenylketonuria were evaluated. The study included 60 children with phenylketonuria and 30 control subjects. Children with phenylketonuria were divided into hyperphenylalaninemia (HPA) and amino acid mixture (AAM) groups. The HPA group had significantly lower levels of GSH-Px, CAT, GSH, TAS, α-aminobutyric acid, and taurine levels (p < 0.01, p < 0.05, p < 0.05, p < 0.001, p < 0.01, p < 0.05, respectively) than the control group. Additionally, the AAM group had significantly lower levels of CAT, TAS, and phylloquinones (p < 0.05, p < 0.05, p < 0.05, respectively) than the control group. It was observed in our study that in the HPA group, a significantly strong positive linear correlation was observed between phenylalanine and α-aminoadipic acid (r = 0.777; p = 0.002). It was concluded that the levels of α-aminoadipic acid and phylloquinone might be an appropriate choice for the determination of phenylketonuria in parallel with the levels of phenylalanine. α-aminobutyric acid and phylloquinone as a supplement can decrease HPA damage.