Mercury ion (Hg2+) is considered to be one of the most toxic heavy metal ions and can cause adverse effects on kidney function, the central nervous system, and the immune system. Therefore, it is important to develop a fast and simple method for sensitive and selective detection of Hg2+ in the environment. This research proposes a portable electrochemical sensor for rapid and selective detection of Hg2+. The sensor platform is designed based on thymine acetic acid anchored with cysteamine-conjugated core shell Fe3O4@Au nanoparticles (Fe3O4@Au/CA/T-COOH) immobilized on a sensing area of a screen-printed carbon electrode (SPCE) with the aid of an external magnetic field embedded in a homemade electrode holder for ease of handling. In the presence of Hg2+, the immobilized thymine combines specifically with Hg2+ and forms a thymine-Hg2+-thymine mismatch (T-Hg2+-T). The resulting amount of Hg2+ was determined by differential pulse anodic stripping voltammetry (DPASV). Under optimal conditions, the sensor exhibited two wide linearities in a range from 1 to 200 μg L-1 and 200-2200 μg L-1 with the reliability coefficient of determination of 0.997 and 0.999, respectively. The detection limit (LOD) and the quantification limit (LOQ) were also determined to be 0.5 μg L-1 and 1.0 μg L-1, respectively. The sensor was further applied for determination of Hg2+ in water samples, a certified reference material and fish samples. The results were compared with flow injection atomic spectroscopy-inductively coupled plasma-optical emission spectroscopy (FIAS-ICP-OES) systems as a reference method. Results obtained with the proposed sensor were relatively satisfactory, and they showed no significant differences at a 95% confidence level by t-test from the standard method. Therefore, considering its fast and simple advantages, this novel strategy provides a potential platform for construction of a Hg2+ electrochemical sensor.