Controlling vector borne disease insects control such as mosquitoes and reducing the use of synthetic insecticides is a major public health challenge. Green nanoinsecticides are suitable alternatives to synthetic insecticides, enabling effective and safer insect control. This study aimed to develop neem oil-based nanoemulsions using Tween 80 and/or gum arabic (GA) as a natural emulsifiers and to study their larvicidal, and adulticidal activity against Culex pipiens. The fatty acids in the oil were identified using gas chromatographs-mass spectrometry (GC-MS). We also studied the acute oral toxicity on male rats and its ecotoxicological effects using the Microtox® assay. We fabricated neem oil nanoemulsions with and without GA at different ratios and performed physicochemical, stability, and characterization studies. The results showed that the major fatty acids in neem oil were oleic acid (44.79%), linoleic acid (18.41%), palmitic acid (18%), and stearic acid (16.64%). We created two highly stable nanoemulsions, i.e., samples 2C and 6C with a droplet sizes of 87.4 and 146.7 nm by mixing neem oil, GA, and Tween 80 at a ratio of 1:0:1.5, and 1:1.5:0, respectively, followed by sonication for 10 min. The lethal concentration (LC50) of neem oil, 2C and 6C were 9.36, 6.45, and 8.01 μg/ml for the Culex pipiens larvae and 21.7, 8.8 and 17.2 μg/ml for the adults. The toxicity time (T50) was 40.7, 10.0, and 28.9 min for normal neem oil, samples 2C and 6C, respectively. The nanoemulsions altered the toxifying-detoxifying enzymes acetylcholinesterase (AChE) and glutathione S-transferase (GST) in Culex pipiens larvae without showing any toxicity in the male rats or the Microtox assay. The neem oil nanoformulations with Tween 80 or GA were highly stable and effective against larval and adult Culex pipiens. GA is a natural-surfactant and hence, is excellent emulsifier alternative to synthetic surfactants. The nanoemulsions did not display any toxic and eco-toxic effects. Therefore, these nanoemulsions can be considered potential alternatives to synthetic insecticides for controlling vector-borne disease insects.