As a global scale pollutant, mercury poses serious risks for human health and the environment; thus, it is of critical importance to develop a simple and efficient sensing protocol to achieve the precise detection of Hg(II). Here we report on the facile fabrication of electro-synthesized FeOOH nanoflakes on nanoporous gold (NPG) microwires. The resulting FeOOH/NPG microelectrode was applied to the electrochemical detection of Hg(II) via square wave voltammetry (SWV). Nanoporous gold microwires with 3D network structures can provide a large specific surface area, facilitate analyte transport and electron transfer, and enhance the electro-catalytical activity of FeOOH-Au. Meanwhile FeOOH nanoflakes, with high adsorption capacities can accumulate analytes onto the electrode surface. Under the optimized conditions, excellent electrochemical performance was achieved with a high sensitivity of 123.5 μA μM−1 cm-2 and low detection limit of 7.81 nM, respectively. In addition, no obvious interference from common ions (e.g., Cu(II), Pb(II), Cd(II)) was observed, and the FeOOH/NPG microelectrode demonstrated exceptional stability. Furthermore, the fabricated electrochemical sensor could be utilized for the detection of Hg(II) in tap water and lake water samples.