DFT at B3LYP/6-31G (d,p) level calculation results for the amine-catalysed isomerization of dimethyl maleate revealed that the mechanism proceeds via four steps: (1) a concerted proton transfer from one amine molecule to another which subsequently enhances the addition of the adduct thus formed to the C–C double bond to yield INT1. (2) ion of a proton from the β-carbon of INT1 by a second amine molecule to give intermediate INT2. (3) Rotation about the C–C single bond followed by proton abstraction by an amine molecule to yield unstable INT3, and (4) an elimination of an amine molecule to yield the trans isomer, dimethyl fumarate. Furthermore, it was found that step 1 is the rate limiting step. However, the activation energy difference between steps 1 and 2 was significantly low and its value depends on the amine catalyst used. The activation energy was found to be lower in water when compared to that calculated in the gas phase. In addition, linear correlation was found between the amine-catalysed isomerization experimental rate and the pKa of the amine catalyst on one hand and the enthalpic and free activation energies on the other hand. The calculations also confirmed that the reaction is first order in dimethyl maleate, second order in the amine catalyst and overall third order. This study disproves three of the four different intermediates that were previously suggested to explain the amine catalysed isomerization of dialkyl maleates. The study verifies the intermediate suggested by Rappoport.