We have constructed an in‐laboratory stopped‐flow extended x‐ray absorption fine structure (EXAFS) apparatus by combining laboratory EXAFS equipment in the dispersive mode and a stopped‐flow unit with two 150‐&mgr;m‐thick boron nitride windows. The rotating anode x‐ray generator with a Mo target was used as an x‐ray source. The self‐scanning photodiode array was adopted as a position sensitive‐linear x‐ray detector. In order to obtain a suitable x‐ray flux intensity, the accumulation of weak intensities during a short gate time was carried out by repeating the measurements. We have confirmed the performance of our apparatus by repeatedly measuring a number of static EXAFS spectra of 0.20 mol dm−3aqueous solution of copper(II) sulfate. By use of our newly developed apparatus, we have succeeded in the direct determination of the structure of the reaction intermediate, the heterodinuclear copper(II)/mercury(II) complex, formed in the copper(II) ion incorporation into the homodinuclear mercury(II) complex of 5,10,15,20‐tetrakis(4‐sulfonatophenyl)porphine.