The fruit and other parts of Momordica cymbalaria are known to have medicinal properties. The study investigates the chemical composition and functional groups of Momordica cymbalaria fruits to assess the insecticidal potential of its bioactive metabolites. In‐silico approach was used to understand the mechanism behind the insecticidal nature of these metabolites. Ethyl acetate extract has 18 compounds while 20 compounds were identified in methanol using GC‐MS analysis. The extracts contain several functional groups, including alkanes, esters, carboxylic acids, amides, and aromatic groups. The insecticidal bioassay using methanol and ethyl acetate extracts of Momordica cymbalaria on Aedes aegypti and Culex quinquefasciatus mosquito larvae shows the LC50 value for Aedes aegypti was 65.7 ppm and for Culex quinquefasciatus was 96.9 ppm for ethyl acetate and methanol extract is 282.36 ppm, 388.09 ppm. Molecular docking of secondary metabolites was performed with five insect proteins, namely OBP, CYP450, PPO, aaNAT and SCP. Results show that Methyl 6‐cis, 9‐cis, 11‐trans‐octadecatrienoate has high binding affinity with SCP‐2 besides showing binding with other insect proteins. The data suggest that Methyl 6‐cis, 9‐cis, 11‐trans‐octadecatrienoate has multiple insecticidal actions and may serve as a green insecticide.