Timing skew between measurement channels can introduce an intolerable error in the power loss measurement, making it challenging to verify the performance of magnetic components while operating in the desired condition. This paper presents a novel approach for in-situ core loss measurement under a rectangular voltage excitation. Mathematical models are built to analyze the effect of timing skew on the measured core loss. An additional capacitor will be utilized to introduce a special geometric feature to the mathematical model, facilitating the determination of the actual timing skew and core loss. Theoretical analysis is verified in simulation and experiment.