This work describes an extension of a Fourier finite element method used for the simulation of three-dimensional (3D) marine controlled source electromagnetic (CSEM) measurements using a secondary field based formulation. The key point here is that the primary field employs a semi-analytical onedimensional (1D) solution rather than the traditional solution over a homogeneous space. Thus, there is no need to heavily discretize the areas surrounding the source nor the solution produced by the background 1D layered formation. In that way, the focus is only on 2D and 3D effects, leading to a better approximation of the solution using a coarser discretization (fewer elements and number of Fourier modes). Numerical results show that savings on this Fourier finite element method due to the use of the proposed secondary field formulation are as large as 87% in terms of the number of unknowns, without any sacrifice in accuracy.