This study analyzes the inhibitory effects of newly synthesized compounds of the K1–12 series on acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes comparatively using IC50 and Kᵢ parameters. Initially, a series of novel 5-fluoroindolylmethylene hydrazone derivatives (K1–12) were designed and synthesized. The structures of the synthesized compounds were elucidated using 1H and 13C NMR spectroscopy as well as mass spectrometric analyses. Subsequently, their inhibitory effects on AChE and BChE were evaluated in vitro . Molecular docking studies performed for all compounds with AChE and BChE enzymes, and pi interactions and conventional hydrogen bonds were involved in protein-ligand interactions. The molecular dynamics (MD) simulation study of the compound with the highest binding potential to the AChE and BChE structures, K10, disclosed that the complexes obtained from docking would be stable. Moreover, the compound is predicted to have a greater tendency to remain within the binding site of the BChE structure. The density functional theory (DFT) study resulted in similar levels of chemical stability and reactivity for the relatively active compounds. The findings revealed that, especially, the K5 and K10 compounds exhibited higher inhibitory activity than donepezil against BChE and AChE, respectively. The results indicate that these compounds could be potential agents for the treatment of neurodegenerative diseases in the future.