Based on the unique electronic properties and high surface area of carbon nanotubes as well as the chemical interaction between thiol group and Hg(II), a novel electrochemical sensor for the determination of Hg(II) in water was fabricated by the immobilization of thiophenol functionalized single-walled carbon nanotubes (SWCNT-PhSH) onto the gold electrode surface. Various factors such as pH, preconcentration time, deposition potential, and deposition time influencing the determination of Hg(II) were thoroughly investigated in this study. Under optimal conditions, the electrochemical sensor exhibited a wider linearity range from 5.0nM to 90nM Hg(II) with a detection limit of 3.0nM (S/N=3). Interferences from other heavy metal ions such as Cr(II), Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II) ions associated with Hg(II) analysis were effectively inhibited. This novel sensor was successfully applied to determine Hg(II) in real water samples with good recovery, ranging from 97–103%. The analytical performance of the as-fabricated electrochemical sensor is superior to most existing sensors.