The management of pests is facing economic and ecological challenges worldwide due to environmental and health hazards caused by most chemical synthetic pesticides. Effective safe alternatives are needed as botanical extracts with significant insecticidal activity. In the present work, zinc oxide (ZnO) and selenium nanoparticles (SeNPs) were synthesized via green approaches using Achillea fragrantissima (Forssk.) Sch.Bip extract.  The particle size and the zeta potential of prepared NPs formulations were characterized by the transmission electron microscope (TEM) and dynamic light scattering (DLS). Then, the efficacy of green synthesized ZnONPs and SeNPs was evaluated against the 3^rd instar larvae of Culex pipiens Linnaeus, 1758, which is considered a disease vector. The larvicidal activity of SeNPs against the 3^rd instar larvae of Cx. pipiens appear to be more potent than ZnONPs and A. fragrantissima extract. The LC₅₀ values after 48 hrs of exposure recorded 0.07, 23.74  and 89.99 ppm for SeNPs, ZnONPs  and  A. fragrantissima extract, respectively. In addition, the fecundity of females who emerged from treated larvae with SeNPs, ZnONPs was significantly affected compared to the control.  Furthermore, the total metabolites and enzymatic activities were greatly affected in all tested stages of Cx. pipiens. Severe ultrastructural deformities were observed in the midgut of treated Cx. pipiens larvae. Overall, the nano-formulations of A. fragrantissima improve their potencies more than the A. fragrantissima extract only.