In the separation and determination of trace amounts of drugs in aqueous samples, there is a major challenge in synthesizing highly efficient, cost‐effective, and easy‐to‐use adsorbents based on natural polymers, which are also biocompatible and biodegradable. In the proposed method, magnetite nanoparticles (Fe3O4) on chitosan (as the carrier) modified with β‐cyclodextrin (BCD) were used as a suitable adsorbent for the pre‐concentration and solid‐phase extraction of trace amounts of Amitriptyline HCl (hydrochloride). Ultraviolet spectrophotometer (λ = 236 nm) was the main instrument used for analyte detection and quantification. Moreover, X‐ray diffraction, Fourier transform infrared spectroscopy, Field Emission Scanning Electron Microscopy, and Energy‐Dispersive X‐ray were used for the identification and characterization of the structure and morphology of the adsorbent and to establish the formation of the synthesized magnetic nanosorbents, as well as to confirm the analyte binding to the adsorbent. Experimental variables affecting the extraction/pre‐concentration and determination of the analyte were investigated and optimized; pH of the sample solution, the amount of NaCl salt (in terms of ionic strength of the solution), the amount of adsorbent, temperature, adsorption time, and volume of the eluent (methanol) were the optimized parameters. Finally, the method was successfully applied for the determination of spiked Amitriptyline hydrochloride (HCl) in tap water and human urine samples. Also, High‐Performance Liquid Chromatography was performed on the aqueous samples to compare the proposed method with the USP (the United States Pharmacopeia) standard method of Amitriptyline HCl assay and after performing a t‐test (confidence level of 95%), no significant difference was observed between the two methods. High accuracy and precision (RSD = 3.91%), High analysis speed, few limitations, low expenses, pure extracted analyte, and low waste were the advantages of this method. This method was also compatible with many existing device methods. Under the optimized experimental conditions, the calibration graph was linear in the range of 0.183 to 50 mg.L−1 with a correlation coefficient of 0.996. RSD of the method was 3.91%, the limit of detection was 37.8 µg.L−1, the maximum sorption capacity of the adsorbent for Amitriptyline hydrochloride was 306.525 mg.g−1 and the preconcentration factor was 3.61. Eventually, the proposed method was compared to other methods that have been performed for the determination of Amitriptyline hydrochloride.