In this paper, a Gaussian process regression (GPR)-based novel method is proposed for non-linear aerodynamic modelling of the aircraft using flight data. This data-driven regression approach uses the kernel-based probabilistic model to predict the non-linearity. The efficacy of this method is examined and validated by estimating force and moment coefficients using research aircraft flight data. Estimated coefficients of aerodynamic force and moment using GPR method are compared with the estimated coefficients using maximum-likelihood estimation (MLE) method. Estimated coefficients from the GPR method are statistically analysed and found to be at par with estimated coefficients from MLE, which is popularly used as a conventional method. GPR approach does not require to solve the complex equations of motion. GPR further can be directed for the generalised applications in the area of aeroelasticity, load estimation, and optimisation.