Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by memory impairment and cognitive decline, largely associated with reduced acetylcholine levels in the brain. Targeting the enzymes responsible for acetylcholine degradation, AChE and BChE remains a central therapeutic strategy for symptomatic management. In this context, a novel series of caffeine-based derivatives incorporating biologically relevant pyridine moieties was rationally designed based on structural features essential for AChE and BChE inhibition. The compounds were efficiently synthesized via nucleophilic substitution reactions between theophylline and halogenated pyridine intermediates under microwave-assisted conditions, which significantly reduced reaction time and enhanced yields up to 95%. Structural elucidation was confirmed by fourier transform infrared (FTIR), nuclear magnetic resonance (NMR), and mass spectrometric (MS) analyses, further supported by density functional theory (DFT) calculations. Molecular electrostatic potential (MEP) mapping was performed to identify electrophilic and nucleophilic regions, while while highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO–LUMO) energy gap analysis and related quantum descriptors provided insight into charge transfer behavior and molecular stability. Natural bond orbital (NBO) and mulliken charge analyses were also employed to elucidate the electronic distributions within the molecules. Additionally, the synthesized derivatives showed preferential inhibition of BChE, with compound 3d exhibiting the most potent activity (IC
50
= 7.87 ± 0.04 μM). This BChE selectivity contrasts with galantamine, a standard AChE inhibitor, and was further validated through molecular docking studies, which revealed favorable and specific binding interactions within the BChE active site. Computational ADMET (absorption, distribution, metabolism, excretion, & toxicity) predictions also indicated good oral bioavailability and a favorable safety profile, highlighting the potential of these novel molecules as selective cholinesterase inhibitors with promising pharmacokinetic properties for Alzheimer’s therapy.