Many phytopathogenic fungi cause a variety of plant diseases which can seriously damage a number of significant crops worldwide. In agricultural and food safety, nanomaterials have become significant for the development of novel antifungal agents that exhibit greater efficacy at lower concentrations than chemical fungicides. In this research, boron/selenium nanoparticles (B/Se NPs) were synthesized via radical polymerization using polyvinyl pyrrolidone (PVP) and tested for their inhibitory effect against two phytopathogenic fungi, Alternaria alternata and Fusarium equiseti, isolated from diseased rice plants and identified morphologically and molecularly. The nanostructure of PVP-loaded B/Se core shell was prepared and confirmed using HRTEM. The size distribution for the nanoparticles ranges between 8.74 and 12.23 nm. The morphology was shown via SEM imaging for the PVP-loaded B/Se sample in cross-section mode. Moreover, their elemental composition analysis was achieved via EDS, and functional structure was confirmed by FTIR spectroscopy. The strong antifungal activity of B/Se NPs was against A. alternata (49 ± 0.57 mm) with MIC of 3.125/0.938 mg mL