Fungi have the ability to act as a biocontrol agent against plant diseases, providing an alternative to chemical control. The objective of this study was to demonstrate the in vitro antifungal activity of the crude extracts of Penicillium citrinum, against two phytopathogens of agronomic importance, Fusarium oxysporum and Sclerotinia sclerotiorum, and identify the metabolites of the most bioactive extract. Chloroform extract of rice solid medium showed excellent growth inhibition activity (65–100%) on two phytopathogens. This extract inhibited 86.9% and 100% of F. oxysporum and S. sclerotiorum, respectively. The metabolites citrinin, citrinin H–1, fusarindin, redoxcitrinin, emodin, 2,4–dihydroxy–3,5,6–trimethylbenzoic acid, sclerotinin A, and 2,4,5–trimethylbenzene–1,3–diol were identified from chloroform extract by LC–HRMS. The metabolite fusarindin was identified for the first time in the fungal species. The use of organic extracts has the potential for successful biological control, mitigating the excessive use of fungicides that may pose a risk to human health and the environment.