Selenium (Se) is an essential trace element that plays a critical role in maintaining human physiological metabolism. Among its various forms, selenium nanoparticles (SeNPs) have been found to possess higher degree of bioavailability and lower toxicity. This study screened 21 probiotics and identified a Se(IV)-resistant strain of Lacticaseibacillus paracasei SCFF20 that effectively converts sodium selenite (Na2SeO3) to SeNPs. The SeNPs produced by L. paracasei SCFF20 were purified, freeze-dried, and systematically characterized using SEM-EDX, DLS, XRD, Raman spectroscopy, and FTIR techniques. SEM–EDX analysis revealed that Se was the primary constituent of the biogenic nanoparticles. The synthesized SeNPs were spherical and polydisperse, with an average particle size of approximately 500.62 nm. XRD patterns and Raman spectroscopy confirmed the biologically amorphous nature of the fabricated nanoparticles. Additionally, FTIR spectral analyses demonstrated the presence of proteins, exopolysaccharides, and lipids coating the surface of the SeNPs. Moreover, the reduction rate of SeNPs, as measured by ICP-OES, was determined to be 91.42%. The findings of this study highlight the potential of L. paracasei SCFF20 as a probiotic capable of producing SeNPs, which can be used as a bio-factory for the safe production of biogenic SeNPs for nutritional supplements and functional foods.