We detected a case of 6-pyruvoyl tetrahydropterin synthase (PTPS) deficiency during a neonatal mass screening and considered the differentiation and treatment of the peripheral form of PTPS deficiency. Although single treatment of BH4 had been started, because of the lowered biopterin (B) value, elevated neopterin (N) value, and N/B ratio in the cerebrospinal fluid (CSF), the peripheral form was judged negative and combined treatment with L-dopa and 5-hydroxy tryptophan (5-HTP) was started. Follow-up study will be necessary to confirm the diagnosis of PTPS deficiency.