In this study, an experiment was conducted to establish a technique to quantitatively measure the flow boiling heat transfer fluctuations in a rectangular minichannel with high spatio-temporal resolution. An infrared (IR) transparent window material, calcium fluoride (CaF₂), was installed on the wall of a rectangular minichannel with a cross section of 2 mm × 2 mm. A thin film of indium tin oxide (ITO), which is transparent to visible-light, was deposited on the minichannel wall side of the IR transparent window material. This visible-light transparent wall allows a high-speed visible camera to capture the behavior of flow boiling from outside the minichannel. Since the ITO film on the wall does not transmit IR radiation, a high-speed IR camera (2000 fps, 0.03 mm/pixel) can be used to measure wall temperature fluctuations. Using the measured wall temperature fluctuations as a boundary condition, heat flux fluctuations due to flow boiling were calculated from unsteady three-dimensional heat conduction analysis inside the wall. The flow boiling pattern changed with time between bubble flow and slug flow. In the bubble flow, bubbles were actively formed at the corners of the minichannel, and the local wall heat flux increased instantaneously and rapidly at the bubble formation points. A plug bubble was formed by the growth and coalescence of the bubbles. In the slug flow, distinctive heat flux fluctuations were observed due to the formation of a thin liquid film, drypatch formation, rewetting of the drypatch, and transition to liquid phase flow. Furthermore, the flow boiling heat transfer obtained from the measurement was classified into five fundamental processes (thin liquid film evaporation, triple contact line, dryout, rewetting, and forced convection), and the contribution of each process was investigated. As a result, we confirmed that the contribution of each process changes corresponding to the flow boiling pattern and that thin liquid film evaporation contributes significantly to the total heat transfer.