When waxy barley (WB) is milled, 40% of the weight is typically discarded as bran. To utilize WB bran resources and improve health functionality, flours prepared from inner bran (IB) and outer bran (OB) layers were used to substitute partially wheat all-purpose flour (APF) for noodle preparation. The dough and noodle qualities were investigated based on analytical tests and sensory evaluations. Both methods revealed considerable darkening of the doughs and noodles upon OB substitution. Boiled noodles with 30% and 50% IB substitution had considerably lower total energy and breaking stress, whereas those with OB substitution had higher breaking stress at all substitution rates. Texture differences between sample groups were observed using analytical tests, but not via sensory evaluation. In addition, the boiled noodles with 50% OB demonstrated considerably lower taste preference in the sensory evaluation than the APF noodles. The comprehensive evaluation score was considerably lower for the boiled noodles with 30% or 50% OB than that of the APF noodles. The β-glucan and antioxidant contents increased with the IB or OB substitution rates. These findings show that APF can be substituted with IB at a substitution rate of 50%, while the substitution of OBF is limited to ≤10%.