Here, we evaluated the application of near-infrared (NIR) spectroscopy for estimating the degradation level of archeological wood samples from the Tohyamago area, the dendrochronological ages of which were also determined. The wood samples were radially cut from three logs obtained from the Tohyamago area. NIR reflectance spectra were measured from the tangential faces of air- and oven-dried wood samples using a Fourier transform NIR spectrophotometer. The second derivative spectra within the wavenumber range of 6400–5200 cm−1, in which the effect of moisture content in wood is suspected to be insignificant, showed a characteristic behavior with age. By comparing the second derivative spectral change in our wood samples with that in wood degraded by aging, thermal treatment, fungal attack, and lightning reported in the literature, we found that the second derivative spectra of wood samples from one log was similar to those of wood degraded by hygro-thermal treatment, whereas those of wood samples from another log was similar to those of wood degraded by brown-rot fungi. The physical and chemical properties of archeological wood were well predicted using a combination of partial least square regression analysis and NIR spectroscopy.