Background Murraya koenigii (L.) Spreng. (Rutaceae) is an evergreen shrub distributed over the sub-tropical to lower temperate climatic zone of Nepal which has been used as spice in culinary practice and traditionally being used to treat bites of poisonous animals, dysentery, skin diseases, vomiting, diarrhea, and inflammations. Objective The main objective of this study is to study the enzyme inhibition potential of different extracts of M. koenigii leaves collected from western Nepal. Methods Total flavonoid content, total phenolic content, in vitro antioxidant, α-amylase, lipase, elastase, tyrosinase, and cholinesterase inhibition activities analysis of M. koenigii in ethyl acetate, methanol, and water extract were evaluated. In addition, high-resolution mass spectrometry-based profiling of flavonoid molecules and their docking analysis were performed. Results Results revealed the noteworthy radical scavenging activity of ethyl acetate extract against ABTS and DPPH. Among the analyzed enzymes, M. koenigii extracts revealed the highest inhibitory potential towards acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) and only water extract showed the inhibition of tyrosinase. The HPLC-ESI-QTOF-MS analysis revealed the presence of Rutin, Quercetin, Ferulic acid, Hyperoside, Kaempferol-7-O-glucoside, and Morin in M. koenigii. Further, in silico docking analysis revealed the significant binding energy of these flavonoid molecules; especially Rutin with BChE. Conclusion The ethyl acetate and methanolic extracts of M. koenigii showed paramount flavonoid and phenolic content along with noteworthy potential towards the inhibition of neuro-degradative enzymes such as BChE which can be characterized further for pharmacological applications. Further study on the isolation of metabolites and their pharmacological properties from M. koenigii is recommended.