Mosquito-borne diseases remain a significant health concern amidst current microbial outbreaks. Phytochemicals offer environmentally safe, biodegradable, and targeted pest management. Nanostructure lipid carriers (NLCs), a second generation of solid lipid nanoparticles, are gaining attention as potential diagnostic and therapeutic tools. Sesbania leaves, rich in fatty acids, phenolics, and terpenes, were analyzed using gas chromatography–mass spectrometry. Magnetic nanoparticles (Se-NLC-MNPs) modified the surface of Sesbania extract, encapsulated in the NLC. The resulting nanoparticles were 129.2 and 218.5 nm in size, with zeta potentials of −6.20 and 43.9 mV, respectively. Transmission electron microscopy showed spherical and oval shapes. XRD patterns confirmed the successful decoration of the NLC with the magnetic nanoparticles. The Sesbania extract (Se) and its nanoparticle conjugates were tested for larvicidal efficacy against Culex pipiens and Musca domestica larvae, at doses ranging from 50 to 1500 ppm and 0.1 to 5 mg/mL. Se-NLC-MNPs showed higher larval mortality rates compared to their Se formulation extracts, achieving 100% mortality in third-instar larvae. Sesbania methanol extract contained more terpenes, fatty acids, and other organic compounds than the aqueous extract, making it more harmful to insect larvae. In terms of relative toxicity, Se-NLC-MNPs were more effective than Se-NLC. An in vitro cytotoxicity assay against the WI38 cell line indicated the cytotoxicity assay, suggesting the potential for these nanoparticles to develop into high-performance, environmentally acceptable therapeutics for mosquito-borne diseases.