The performance of some Fourier transform based fundamental current detection algorithms is evaluated and compared in this paper. Some difficult conditions are imposed by a load which draws a highly distorted current with a slight fluctuation, i. e. with non-equal semi-periods. The implemented algorithms are Recursive Discrete Fourier Transform (RDFT), Discrete Fourier Transform (DFT) implemented through a Finite Impulse Response (FIR) filter and respectively the Fast Fourier Transform (FFT) with Butterfly operation and radix-2 decimation in time (DIT). A digital signal processor (DSP) based solution is used for real-time implementation, namely a dSPACE 1103 controller development board. MATLAB/Simulink software is used for the design of the algorithms because it provides specialized tools and blocks. For the performance comparison one used criteria like total harmonic distortion (THD) and settling time of detected fundamental current and also the run time for the DSP. This study may be useful as a guide for engineers in selecting the suitable Fourier transform based control algorithm for active power filters or other grid-synchronized equipments which are operating in difficult load conditions.