We investigated fungal communities in oak wounds to determine how fungal species richness and community composition changes depending on the age of wounds. The sampling of wood cores was carried out from 10-, 20-, 30-, 40-, and 50-year-old wounds. The fungal community was analyzed using high-throughput sequencing of ITS2 rDNA. Sequence analysis showed the presence of 534 fungal OTUs, which were 83.4% Ascomycota, 16.3% Basidiomycota, and 0.3% Mucoromycota. The fungal OTU richness changed over time: it increased as compared between 10- and 20-year-old wounds, remained similar in 20- to 40-year-old wounds, and decreased in 50-year-old wounds. The fungal community composition also changed over time with the largest differences detected between 10-year-old and older wounds (p < 0.001). The most common representatives of Basidiomycota were Laetiporus sulphureus (34.7%), Mycena galericulata (17.0%), and Cylindrobasidium evolvens (6.5%), and the most common of Ascomycota were Aposphaeria corallinolutea (13.6%), Sclerostagonospora cycadis (7.6%), and Cadophora malorum (5.8%). In conclusion, oak wounds of different ages were colonized by a high diversity of fungi including oak-associated species. Fungal communities in oak wounds underwent qualitative and quantitative changes over time, which led to the gradual shift from fungal generalists in young wounds to oak specialists in older wounds.