In the design study of an advanced sodium-cooled fast reactor (advanced-SFR) in Japan Atomic Energy Agency (JAEA), the use of a specific fuel assembly (FA) with an inner duct structure called fuel assembly with an inner duct structure (FAIDUS) has been investigated to enhance safety of Advanced-SFR. Due to the asymmetric layout of fuel rods by the inner duct, it is necessary to estimate the coolant temperature distribution to confirm feasibility of FAIDUS. In JAEA, an in-house subchannel analysis code named thermal-hydraulic analysis of asymmetrical flow in reactor elements (ASFRE) has been developed as a FA design tool. For the typical FAs, the numerical results of ASFRE had been validated by comparisons with experimental data, in the previous study. As for the FAIDUS, confirmation of validity of the numerical results by ASFRE was not enough because the reference data on the thermal hydraulics in FAIDUS have not been obtained by the mockup experiment, yet. In this paper, therefore, the code-to-code comparisons with numerical results of ASFRE and those of an in-house computational fluid dynamics (CFD) code named single-phase thermal-hydraulic analysis in an irregular rod array layout (SPIRAL) were applied to make further discussion on applicability of ASFRE to the thermal hydraulics analysis in FAIDUS. Thermal hydraulic analyses of a typical FA and FAIDUS at high and low flowrate conditions were conducted. The applicability of ASFRE was indicated through the confirmation of the consistency of mechanism on appearance of the specific temperature distributions between the numerical results by ASFRE and those by SPIRAL. In addition, the necessity of modification on the empirical constants in numerical model of ASFRE to improve the predictive accuracy was indicated.