In this study, a selective method for the determination of atropine in pharmaceutical formulations was proposed. L-cysteine capped Mn-doped ZnS quantum dots (QDs) were prepared in an in-situ method using sodium thiosulfate precursor and characterized by spectrofluorometer, Fourier transform infrared spectroscopy (FT-IR), transmission electron microscope (TEM) and X-ray diffractometer (XRD). Dopamine hydrochloride was used as a precursor for preparation of poly dopamine-coated molecularly imprinted Mn-doped ZnS quantum dots. Finally, these prepared molecularly imprinted Mn-doped ZnS quantum dots were used for determination of atropine in pharmaceutical formulations. The obtained linear range for determination of atropine was in the range of 2 × 10−8 – 7 × 10−6 M, with a correlation coefficient (R2) of 0.9889; and the detection limit (S/N = 3) was 3.2 nM.