Background: Over the past 20 years, the Contour Method (CM) has been extensively implemented to evaluate residual stress at the macro scale, especially in products where material processing is involved. Despite this, insufficient attention has been devoted to addressing the problems of input data filtering and residual stress uncertainties quantification. Objective: The present research aims to tackle this fundamental issue by combining Gaussian Process Regression (GPR) with the CM. Thanks to its stochastic nature, GPR associates a Gaussian distribution with every subset of data, thus holding the potential to model the inherent uncertainty of the input data set and to link it to the measurements and the surface roughness. Methods: The conventional and unrobust spline smoothing process is effectively replaced by the GPR which is capable of providing uncertainties over the fitting. Indeed, the GPR stochastically and automatically identifies the fitting parameter, thus making the experimental data post-processing practically unaffected by the user’s experience. Moreover, the final residual stress uncertainty is efficiently evaluated through an optimised Monte Carlo Finite Element simulation, by appropriately perturbing the input dataset according to the GPR predictions. Results: The simulation is globally optimised exploiting numerical techniques, such as LU-factorisation, and developing an on-line convergence criterion. In order to show the capability of the presented approach, a Friction Stir Welded plate is considered as a case study. For this problem, it was shown how residual stress and its uncertainty can be accurately evaluated in approximately 15 minutes using a low-budget personal computer. Conclusions: The method developed herein overcomes the key limitation of the standard spline smoothing approach and this provides a robust and optimised computational framework for routinely evaluating the residual stress and its associated uncertainty. The implications are very significant as the evaluation accuracy of the CM is now taken to a higher level.