The present experiment was conducted to determine whether water extracts of lemon balm and oregano could suppress anthracnose in strawberry and to identify the important secondary metabolites responsible for such activity. Runner plants of three strawberry cultivars (Fragaria × ananassa Duch. ‘Sachinoka’, ‘Akihime’, and ‘Tochiotome’) were treated with water extracts (20%, w/v) of lemon balm (Melissa officinalis L.) and oregano (Origanum vulgare L.) separately and inoculated with Colletotrichum gloeosporioides (C. fructicola, CG1). Two weeks after CG1 inoculation, it was observed that the shoots and roots of the herb extract-treated plants had lower disease incidences and indices compared to those of the control regardless of the cultivar. Consequently, dry weights of the shoots of all the cultivars treated with the herb extracts were observed to be heavier than in the control; similarly, heavier dry weights of roots were also observed in herb extract-treated plants in ‘Sachinoka’ and ‘Tochiotome’. Upon analyzing the results of ultra-performance liquid chromatography-tandem mass spectrometer (UPLC-MS/MS), rosmarinic acid and luteolin in lemon balm and apigenin and protocatechuic acid in oregano were identified to be the metabolites with the highest concentration in their respective plants. In addition, the antifungal effect of all these compounds against CG1 was confirmed by in vitro tests. Thus, it can be concluded that water extracts of lemon balm and oregano could suppress anthracnose in strawberry plants, and the four identified compounds in the extracts could play key roles in the antifungal properties of these herbs.