In this study, an adsorption‐based determination system was designed for protamine. A multi‐walled carbon nanotube (MWCNT), which is a strong adsorbent, was used. The competitive adsorption process between dyes and protamine formed the basis of the sensor system. The adsorption process was followed over the dyes by UV‐vis absorption spectroscopy. The achievability of this sensor system was supported by the thermodynamic parameters. Transmission electron microscopy (TEM) and Fourier Transform infrared spectroscopy (FTIR) techniques were used for characterization of the sensor system. It was determined that the sensor system remained stable at physiological temperature and pH range. Limit of detection (LOD) values of PyB‐COO—MWCNT and PyY‐COO—MWCNT systems were calculated as 1.32 and 1.12 ngml‐1, respectively. The applicability of the sensor systems was demonstrated by operating in bovine serum solutions.