Transmission losses through the building envelope account for a large proportion of building energy balance. One of the most important parameters for determining transmission losses is thermal transmittance. Although thermal transmittance does not take into account dynamic parameters, it is traditionally the most commonly used estimation of transmission losses due to its simplicity and efficiency. It is challenging to estimate the thermal transmittance of an existing building element because thermal properties are commonly unknown or not all the layers that make up the element can be found due to technical-drawing information loss. In such cases, experimental methods are essential, the most common of which is the heat-flux method (HFM). One of the main drawbacks of the HFM is the long measurement duration. This research presents the application of deep learning on HFM results by applying long-short term memory units on temperature difference and measured heat flux. This deep-learning regression problem predicts heat flux after the applied model is properly trained on temperature-difference input, which is backpropagated by measured heat flux. The paper shows the performance of the developed procedure on real-size walls under the simulated environmental conditions, while the possibility of practical application is shown in pilot in-situ measurements.