The non-destructive testing technique of pulsed thermography has been widely used in materials to detect defects due to its low cost, large detection area, and rapid implementation. After conducting experiments, data processing is often necessary to reduce the influences of noise and non-uniform backgrounds and highlight defect information. However, during the analysis, physical information is usually ignored. In addition to thermographic data analysis, numerical simulations are also popular for analytical studies based on physical information, but they don’t fully utilize the experimental data. To address this, a new method was proposed using a physics-informed neural network (PINN) for thermographic data processing. PINN combines the prediction capabilities of deep neural networks with physical laws presented as partial differential equations and boundary conditions, allowing for both experimental data and physics information to be utilized in modelling. In pulsed thermography, the heat transfer is governed by Fourier's law of heat conduction in a three-dimensional system. However, there is a lack of temperature measurements in the depth direction. The proposed method solves this problem by using collocation points generated from Latin hypercube sampling. The PINN model provides a good estimation of the backgrounds in the thermograms, and the features of surface/subsurface defects are highlighted by subtracting the estimated backgrounds from the original thermograms. In the case study, the performance of the proposed method was found to be effective.