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A novel measurement system consisting of scanning electron microscopy and infrared (IR) thermography has been constructed to measure the thermal conductivity and the thermal diffusivity on a micro-/nanometer scale. In this study, we measured them for a stainless-steel wire with a diameter of 50 μm to demonstrate the validity of our system. The time evolution of temperature distribution on the whole of the stainless-steel wire was recorded by the IR thermograph when the wire was irradiated by the electron beam (EB). A time response of the wire temperature corresponding to the on/off of the EB irradiation was clearly observed, indicating that local EB heating was realized. In addition, the experimental time evolution of temperature at its transient phenomena was in good agreement with the theoretical calculation based on a one-dimensional (1D) equivalent-circuit model of heat flow coupled with electric current, where the thermal parameters, such as thermal conductivity and heat capacitance, were set to bulk values. Therefore, it can be concluded that our system is valid to evaluate the thermal conductivity of the 1D wire sample. For evaluating the thermal diffusivity of the wire sample, we applied a periodic EB irradiation by a rectangular wave with a frequency of 0.25 Hz. The thermal diffusivity was evaluated to be (2.8 ± 0.6) × 10−5 m2 s−1, which was seven times as large as that of bulk stainless steel. Our system can be applied to an AC calorimetry method for a 1D system sample after the analysis procedure is further modified.