The effects of low-energy X-ray irradiation were investigated as an intervention strategy for the disinfection of fungi-contaminated woodblocks. Fungi were isolated from the woodblocks of the Nguyen dynasty of Vietnam and Cladosporium sp. was identified as the most radiation-resistant strain in the woodblock. The dose rates of the F1 (1-mm-aluminum filtered) and F0 (non-filtered) X-rays at the surface of the woodblock were 1.14 and 4.64 kGy/h, respectively. At the middle (8.5 mm from the surface) of the woodblock, the doses of the F1 and F0 X-rays decreased to 76% and 20% of the surface doses, respectively. The F1 X-rays were useful for irradiating the inside of the woodblock; the concentration of the fungi at the middle decreased by more than 4 log fractions at 6.2 kGy and the fungi were eliminated with a surface dose of 8.3 kGy. Furthermore, the contaminated fungi in the woodblock were disinfected by both-side irradiation with F1 X-rays delivering a dose of 10 kGy at a dose uniformity of 1.04.