Wood materials for construction purposes can be attacked by various wood-destroying fungi. An ideal wood-preserving substance is supposed to be environment- and health-friendly. For this reason, the effects of the most relevant and non-toxic methylxanthines, such as caffeine and its metabolites theobromine and theophylline, on fungal growth, together with their degradability related to their properties were analyzed in this study. Agar tests with four wood-destroying fungal species (Serpula lacrymans, Coniophora puteana, Gleophyllum sepiarium, and Trametes versicolor) were performed after 28 days of substance exposure. Caffeine exhibited a 100% inhibitive effect on fungal growth, contrary to theobromine, which was not effective in that respect. Theophylline exhibited variable effects on the analyzed fungi. The analysis of degradability indicated the persistence of caffeine and theobromine, but theophylline was degraded up to 34%. The relation of toxicity to chemical structure of studied methylxanthines indicated the dipole moment and lipophilicity as important parameters affecting the antifungal properties. Both caffeine and theophylline are suitable potential candidates for antifungal active substances.