In the inspection of existing bridges, measurement of natural frequency by vibration test is relatively safe and easy. The natural frequency can also be obtained from numerical analysis. In this study, we numerically investigated influence of partial decay of timber members, such as arches and joints between columns and girders, on the natural frequency of deck-type timber arch bridges. Concretely, we estimated sensitivity of the decay parts using the regression plots between natural frequency and magnification to the original Young’s modulus of the decay parts. The results showed that the decay at the part of the vibration antinode was highly sensitive, while the vibration node was low-sensitive. Lastly, we tried to estimate the actual state of decay of the target bridge adjusting parameters, such as Young’s modulus and specific weight, so that the natural frequency could fit the measured value.