Fusarium graminearum, a major causal agent of Fusarium head blight, poses a persistent threat to cereal production and food safety, necessitating the development of sustainable biocontrol strategies as alternatives to chemical fungicides. In the present study, a lactic acid bacterium, Lacticaseibacillus paracasei MYSN17, obtained from the repository of Applied Mycology Laboratory was evaluated for its antifungal activity against F. graminearum MTCC 1893 and the molecular basis underlying its antagonistic activity. MYSN17 demonstrated potent antifungal activity in agar overlay and dual-culture assays, resulting in significant suppression of fungal growth. The cell-free supernatant (CFS) displayed a concentration-dependent inhibition of fungal growth at 20%, resulting in 88.33% inhibition. Scanning electron microscopy revealed morphological alterations on treatment with MYSN17 and its CFS. Further, CFS treatment effectively prevented F. graminearum colonization in maize kernels under storage conditions. LC-MS/MS profiling identified eleven organic acids in the CFS, suggesting a metabolite-mediated mechanism of fungal inhibition. Genome mining revealed putative biosynthetic potential encoding bacteriocins, lantipeptides, non-ribosomal peptide synthetases (NRPS), terpenes, and type III polyketides. Collectively, the findings establish L. paracasei MYSN17 as an eco-friendly biocontrol agent for food preservation and sustainable management of F. graminearum.