This paper studies the dual form of Witten-Dijkgraaf-Verlinde-Verlinde (WDVV) equations in N=2 supersymmetric Yang-Mills theory by applying a duality transformation to WDVV equations. The dual WDVV equations called in this paper are non-linear differential equations satisfied by dual prepotential and are found to have the same form with the original WDVV equations. However, in contrast with the case of weak coupling calculus, the perturbative part of dual prepotential itself does not satisfy the dual WDVV equations. Nevertheless, it is possible to show that the non-perturbative part of dual prepotential can be determined from dual WDVV equations, provided the perturbative part is given. As an example, the SU(4) case is presented. The non-perturbative dual prepotential derived in this way is consistent to the dual prepotential obtained by D'Hoker and Phong.