In this paper, the Fourier-based PLL (Phase-locked Loop) is introduced with a new structure, capable of selective harmonic detection in single and three-phase systems. The application of the FB-PLL to harmonic detection is discussed and a new model applicable to three-phase systems is introduced. An analysis of the convergence of the FB-PLL based on a linear model is presented. Simulation and experimental results are included for performance analysis and to support the theoretical development. The decomposition of an input signal in its harmonic components using the Fourier theory is based on previous knowledge of the signal fundamental frequency, which cannot be easily implemented with input signals with varying frequencies or subjected to phase-angle jumps. In this scenario, the main contribution of this paper is the association of a phase-locked loop system, with a harmonic decomposition and reconstruction method, based on the well-established Fourier theory, to allow for the tracking of the fundamental component and desired harmonics from distorted input signals with a varying frequency, amplitude and phase-angle. The application of the proposed technique in three-phase systems is supported by results obtained under unbalanced and voltage sag conditions.