This paper presents an inverse thermal modeling technique to determine the core losses from the temperature rise inside the transformer core. For this purpose, initially, a customized printed circuit board (PCB) with thermal sensors is used to measure the temperature rise. Afterward, a 3D magneto-thermal forward model is developed to validate the temperature rise. The accuracy of the forward model is checked by comparing the simulated core losses and temperature rise of the transformer with experimental measurements for different supply conditions. The results show that the forward model can accurately estimate the core losses with a maximum relative error of less than 2.7% and predict the temperature rise in the core with a maximum relative error of less than 6.2%. Lastly, after ensuring the accuracy of the forward model, an inverse modeling technique is applied to the 3D thermal model to predict the core losses of the transformer directly from the measured temperature rise. The accuracy of the inverse model in estimating the core losses is checked by comparing the results with experimental measurements. The novel approach for the PCB design besides the inverse model shows that the technique can be applied to estimate the core losses directly from the measured temperature rise inside the core with a relative error of 2.7% compared to experiments.