The purpose of the paper is to show that, in low dimensions, the WDVV equations are bi-Hamiltonian. The invariance of the bi-Hamiltonian formalism is proved for N = 3. More examples in higher dimensions show that the result might hold in general. The invariance group of the bi-Hamiltonian pairs that we find for WDVV equations is the group of projective transformations. The significance of projective invariance of WDVV equations is discussed in detail. The computer algebra programs that were used for calculations throughout the paper are provided in a GitHub repository.