Seeking to characterize and mitigate the adverse effects of misalignment in WPT applications, we present the design and construction of a low-cost wireless charger prototype and a novel phase-shift measurement system. The first is built using a half-bridge inverter and antennas with series-series compensation, while a microcontroller (Teensy 4.1) supplies high-frequency PWM signals. The measurement system comprises high-speed operational amplifiers and an exclusive OR gate. A resistor was used as load. On the other hand, the maximum power transfer efficiency occurs at the resonance frequency, nevertheless, this depends physically on the geometry of the coupling system. Using a 3D-printed displacement system, we created controlled vertical misalignments between the coils, thereby obtaining variations in the resonance frequency of the system and consequently, producing a proportional phase shift between the voltage and current waves of the transmitting antenna. As the experimental results demonstrate, the measurement system can process this high-frequency signal for the phase shift estimation and subsequently use it as a control variable in a proportional-integral controller, which adjusts the operation frequency of the system and brings it back to optimal conditions. This precise yet inexpensive implementation could find its application in EVs and biomedical devices’ efficient wireless chargers.