Reliable and precise quantification of 25‐hydroxyvitamin D3 in clinical samples is vital because vitamin D3 deficiency lead to several disorders, such as mental illness, osteoporosis, and coronavirus disease. Herein, we report the fabrication of a novel electrochemical aptasensor using a nanocomposite, including reduced graphene oxide, pyrrole, and l‐cysteine, for the sensitive detection of 25‐hydroxyvitamin D3. Subsequently, the aptamer of 25‐hydroxyvitamin D3 was immobilized on the surface of the modified electrode. Differential pulse voltammetry signals were utilized for studying the binding and measurement of 25‐hydroxyvitamin D3 based on the oxidation peak. Under the optimum conditions, the designed electrochemical aptasensor exhibited a linear detection range of 0.001–150 nM, with a limit of detection of 0.006 nM. Furthermore, the proposed aptasensor selectively detected 25‐hydroxyvitamin D3 compared to other analogs. Moreover, this aptasensor was successfully applied for the detection of 25‐hydroxyvitamin D3 in human serum samples, which were quantified by the enzyme‐linked immunosorbent assay method. The acceptable recoveries of 82.67%–111.07% demonstrated that this proposed electrochemical aptasensor can be a promising alternative for clinical methods of vitamin D determination.