The application of green nanotechnology in agriculture has been receiving substantial attention, especially in the development of new nano-fertilizers and nano-insecticides. Herein, the metabolites secreted by the fungal strain Penicillium chrysogenum are used as a reducing agent for selenium ions to form selenium nanoparticles (Se-NPs). The synthesized Se-NPs were characterized using color change, UV-Vis spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, transmission electron microscopy (TEM), energy dispersive X-ray (EDX), X-ray diffraction (XRD), and dynamic light scattering (DLS). The biomass filtrate of the fungal strain changed from colorless to a ruby red color after mixing with sodium selenite with a maximum surface plasmon resonance at 262 nm. Data exhibits the successful formation of spherical, amorphous Se-NPs with sizes ranging between 3–15 nm and a weight percentage of 38.52%. The efficacy of Se-NPs on the growth performance of sunflower (Helianthus annuus L.) and inhibition of cutworm Agrotis ipsilon was investigated. The field experiment revealed the potentiality of Se-NPs to enhance the growth parameters and carotenoid content in sunflower, especially at 20 ppm. The chlorophylls, carbohydrates, proteins, phenolic compounds, and free proline contents were markedly promoted in response to Se-NPs concentrations. The antioxidant enzymes (peroxidase, catalase, superoxide dismutase, and polyphenol oxidase) were significantly decreased compared with the control. Data analysis showed that the highest mortality for the 1st, 2nd, 3rd, 4th, and 5th instar larvae of Agrotis ipsilon was achieved at 25 ppm with percentages of 89.7 ± 0.3, 78.3 ± 0.3, 72.3 ± 0.6, 63.7 ± 0.3, and 68.7 ± 0.3 respectively after 72 h.