The physics of dynamic heat flux loading in rotating detonation combustors (RDCs) is crucial due to the highly unsteady heat loading from detonation waves in the combustor annulus. These peak heat load values are significantly higher than those in traditional combustors due to the high combustion intensity. The heat flux in RDCs must be thermally managed with the same propellants used for current air-breathing and rocket combustors, adding strain on the cooling capacity of these propellants to retrofit RDCs. Additionally, the high, spatio-temporally varying heat flux values and harsh aerothermal environments render traditional low-speed sensors ineffective for obtaining reliable heat flux measurements, which are essential for developing cooling strategies for long-duration RDC operation. This study introduces a novel MHz rate-capable heat flux sensor for application in a rotating detonation environment. The sensor utilizes an atomic layer thermopile (ALT) method, where multiple layers of material are sandwiched to produce a transverse Seebeck voltage proportional to the heat flux load. This sensor is demonstrated in this work in an hydrogen-air rotating detonation engine. The sensor provides time-resolved heat flux measurements across a 2 mm (azimuth) sensor area. The results show peak heat flux loading up to 40-50 MJ/m², with periodic heating and cooling in the injection nearfield and constant heating with periodic increase in heatflux during the wave passage, in the far field. These measurements are being compared to data from an unsteady Reynolds-averaged Navier-Stokes (URANS) reactive RDE simulation, showing good agreement in both the near and far fields. Further measurements are ongoing to develop a comprehensive heat flux dataset for future RDE/RDRE applications.