A partial structure of the copper(II) ion of a reaction intermediate at the formation of a copper(II) porphyrin complex in the metal substitution reaction of the mercury(II) porphyrin complex with the copper(II) ion in an aqueous acetate buffer solution has been determined by using a newly developed rapid EXAFS apparatus, which is constructed by combining a stopped-flow and a laboratory-scale EXAFS equipments. The porphyrin used is 5,10,15,20-tetrakis(4-sulfonatophenyl)porphine. Two Cu-N bonds in the reaction intermediate have been found to be 204 pm, which are longer than the Cu-N bonds (200 pm) in the final product of the copper(II) porphyrin complex, and it has been estimated that the copper(II) ion in the intermediate is about 40 pm out from the center of the porphine ring, and thus the mercury(II) and copper(II) ions are almost in contact in the heterodinuclear complex. Since we did not clearly see the Hg...Cu nonbonding interaction in the EXAFS spectrum, the position of the atoms may be significantly fluctuating due to the repulsion between the atoms.