The characterization of a quantum device is a crucial step in the development of quantum experiments. This is accomplished via Quantum Process Tomography, which combines the outcomes of different projective measurements to deliver a possible reconstruction of the underlying process. The tomography is typically performed by processing an overcomplete set of measurements and extracting the process matrix from maximum-likelihood estimation. Here, we introduce a new technique, referred to as Fourier Quantum Process Tomography, which requires a reduced number of measurements, and benchmark its performance against the standard maximum-likelihood approach. Fourier Quantum Process Tomography is based on measuring probability distributions in two conjugate spaces for different state preparations and projections. Exploiting the concept of phase retrieval, our scheme achieves a complete and robust characterization of the setup by processing a near-minimal set of measurements. We experimentally test the technique on different space-dependent polarization transformations, reporting average fidelities higher than 90% and significant computational advantage.