In order to assess antifungal activity of a wooden storage box, which was made of Paulownia tomentosa and used for keeping ancient documents, antifungal activity of volatile organic compounds emitted from the box was investigated along with qualitative analysis on major substances of the compounds. After collecting floating microorganisms inside air tester, the fungal activity was assessed by counting the number of colonies growing on TSA media. Compared to the control which collected 85 colonies from Outdoor, 72 colonies were observed showing reduction rate of 14.82%. Through GC/MS and TDS system analysis, limonene was detected from the volatile organic compounds as characteristic features. When the fungal activity was assessed through fumigation by adding natural biocide BI and BII containing eugenol and anethole as major substances, both biocides showed a strong fungal activity with respectively 92.6%(inside the box) and 99.9%(outdoor) of reduction rate. Although these results didn't clarify antifungal activity of the volatile organic compounds emitted from the Paulownia-wood storage box and their functional components, it was at least confirmed that there is application possibility of natural biocide to use for preservation of ancient documents with increased efficiency in controlling pests of wooden storage boxes.