This article is devoted to the efficient numerical solution of the Helmholtz equation in a two‐ or three‐dimensional (2D or 3D) rectangular domain with an absorbing boundary condition (ABC). The Helmholtz problem is discretized by standard bilinear and trilinear finite elements on an orthogonal mesh yielding a separable system of linear equations. The main key to high performance is to employ the fast Fourier transform (FFT) within a fast direct solver to solve the large separable systems. The computational complexity of the proposed FFT‐based direct solver is O(N log N) operations. Numerical results for both 2D and 3D problems are presented confirming the efficiency of the method discussed.