Hybrid structural electronics (HSE) consists of printed electronics, conventional rigid electronics and load bearing supporting parts of a device (plastic, glass etc.). Extra-large area and flexible lighting elements with embedded light emitting diodes (LEDs) are an example of such applications. LEDs can be used e.g. as light sources to create smart surfaces for the architectural or automotive industry. Once the LEDs are embedded into the structure, they cannot be replaced. In order to make sustainable HSE products with long lifetime, the new type of designs is needed. The elements of HSE undergoes conditions with elevated thermal stresses while in operation. That is known to have an impact on their performance and lifetime, thus making a proper heat management of the LED crucial. Due to the novel additive manufacturing methods, structures, and unconventional material combinations, many thermal management related aspects are not known. In this study, a two-step hybrid method, including thermal modelling and measurements, is utilized to estimate thermal behavior of a surface mounted LED on polymer substrate used in HSE. The model is created and simulated in COMSOL Multiphysics. The validity and accuracy of the model's thermal behavior is verified through measurements with thermal transient measurements. Based on the experimental verification, the proposed simulation model only has small (less than 2 %) temperature variations when compared with measurements. Hence, the developed model can be used as a basis for designing structural LED elements and predicting their performance characteristics in different user cases.