This paper presents the effect of noise on surrogate based stochastic natural frequency analysis of composite laminates. Surrogate based uncertainty quantification has gained immense popularity in recent years due to its computational efficiency. On the other hand, noise is an inevitable factor in every real-life design process and structural response monitoring for any practical system. In this study, a novel algorithm is developed to explore the effect of noise in surrogate based uncertainty quantification approaches. The representative results have been presented for stochastic frequency analysis of spherical composite shallow shells considering Kriging based surrogate model. The finite element formulation for laminated composite shells has been developed based on Mindlin’s theory considering transverse shear deformation. The proposed approach for quantifying the effect of noise is general in nature and therefore, it can be extended to explore other surrogates under the influence of noise.