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Tomato is a globally important fruit crop, which is easily susceptible to infection by plant-parasitic nematodes during growth. In this study, selenium nanoparticles were biosynthesized through the selenite reduction pathway in a wild-type Pseudomonas stutzeri BB19 and were characterized by uniform nanostructured needle-like forms with an average size of 95.2 nm. The nematicidal effect of biosynthesized selenium nanoparticles (BioSeNPs) at different concentrations (2, 6, and 10 ppm) during the pre- or post-infection of tomato root-knot nematode (RKN), Meloidogyne incognita, was assessed under greenhouse conditions. The BioSeNPs were applied as a foliar spray or a soil drench, compared to ethoprophos nematicide (100 mL/pot). The results showed that the ethoprophos nematicide significantly reduced the number of galls, egg mass, and eggs/egg mass of M. incognita by 94.2, 92.8, and 49.8%, respectively. BioSeNPs, as foliar sprays, significantly reduced the number of galls in post-treated infected tomato plants at 10 ppm and in pre-treated infected tomato plants at 2 ppm by 91.9 and 91.4%, respectively. Concerning the egg mass, BioSeNPs significantly reduced it in pre-treated infected tomato plants at 2 ppm as a foliar spray by 90.9%. Moreover, BioSeNPs significantly reduced the eggs/egg mass in pre-treated infected tomato plants at 2 ppm as a soil drench by 43.3%. On the other hand, the BioSeNPs considerably improved tomato growth, chlorophyll a and b, carotenoid content, and enzymes (i.e., catalase and peroxidase) activity compared to untreated infected tomato plants (negative control). Hence, the BioSeNPs show a significant application potential as a cost-effective and environmentally friendly biocontrol agent for RKN management in tomato plants.