Naringenin and naringin, bioactive flavonoids from citrus fruits, exhibit neuroprotective effects, showing promise for neurodegenerative diseases like Alzheimer's and Parkinson's. Additionally, they demonstrate significant anticancer potential, modulating key signaling pathways involved in tumor growth, apoptosis, and metastasis, thus expanding their therapeutic applications in cancer treatment. These compounds interact with nicotinic acetylcholine receptors (nAChRs), a class of ligand-gated ion channels critical for modulating neurotransmission within the central nervous system. In this study, naringenin and naringin were found to selectively inhibit specific subtypes of nAChRs in a concentration-dependent, reversible, and noncompetitive manner. These effects were examined using two-electrode voltage-clamp recordings in Xenopus laevis oocytes heterologously expressing various human nAChR subtypes, and further analyzed by site-directed mutagenesis and molecular docking simulations to identify key binding residues. Mutational analyses, supported by molecular docking, revealed that certain mutations in nAChRs eliminate naringin’s inhibitory effect, highlighting a selective binding affinity. This inhibition was observed selectively in α3β2 and α3β4 nAChR subtypes, which are significant within the autonomic nervous system, while α7 and α4β2 nAChRs, often implicated in neurodegenerative processes, remained unaffected. These findings suggest that naringenin and naringin could be developed as targeted modulators of nAChRs, offering therapeutic potential.