The larvicidal activity of cinnamon oil and its main component, cinnamaldehyde, was compared with their nano-emulsions (NEs) against Culex pipiens mosquito larvae. Oil-in-water (O/W) NEs preparation was based on the coarse emulsion followed by high-energy ultra-sonication. The droplet size, polydispersity index (PDI), viscosity, zeta potential, and pH of NEs were investigated. The droplet sizes of the NEs were 95.67 nm for cinnamon oil and 174.59 nm for cinnamaldehyde. The NEs recorded high negative zeta potentials (-30.0 and -21.20 for cinnamon oil and cinnamaldehyde, respectively). The larvicidal activity results showed that the cinnamaldehyde (LC50 = 94.46 and 72.91 mg/l for T and NE, respectively) had higher activities than cinnamon oil (LC50 = 154.08 and 123.13 mg/l for T and NE, respectively) after 24 h of exposure against C. pipiens larvae. These results proved that NE formulation enhanced the activity of tested compounds against larvae. The in vitro effect on the acetylcholinesterase (AChE), adenosine triphosphatase (ATPase), and gamma-aminobutyric acid transaminase (GABA-T) were demonstrated, and the data proved that the NEs formulations were higher than their pure compounds. Non-formulated cinnamon oil and cinnamaldehyde caused 17.26% and 30.83% of AChE, respectively, while their NEs caused 46.40% and 60.59% inhibition. Furthermore, the molecular docking studies indicated that the affinity binding of cinnamaldehyde on AChE and GABA-T was higher than ATPase. This work describes bio-products with potential use against C. pipiens larvae as eco-friendly products.