In an era where high-frequency flying capacitor (FC) multilevel inverters (MLI) are increasingly gaining attention in energy conversion systems that push the boundaries of power density, the need for a compact, fast, and accurate FC voltage monitoring is also increasing. In this paper we designed and developed a new FC measurement system, based on precise sampling of the inverter switching node voltage, through a bidirectional clamping circuit. The deviation of FC voltages from their nominal values are extracted by solving a set of linear equations. With a single sensor per phase and no isolation requirements, as opposed to dozens of sensors in traditional FC monitoring, our approach results in significantly lower cost, complexity, and circuit-size. Detailed device-level simulations in LTspice and system-scale simulations in Matlab, validate the accuracy and speed of the proposed measurement system and the balancing strategy in steady state, abrupt load change and imbalance conditions. Experiments carried out in a 3-phase Gallium-Nitride 5-level inverter prototype, reveal a gain in precision and bandwidth that is more than 30 times that of conventional methods, at a fraction of their cost and footprint. The recorded performance renders the developed sensor an ideal solution for fast MLIs based on wide-bandgap technology