In the shear-lag analysis of structures deterministic procedure is insufficient to provide complete information. Probabilistic analysis is a holistic approach for analyzing shear-lag effects considering uncertainties in structural parameters. This paper proposes an efficient and accurate algorithm to analyze shear-lag effects of structures with parameter uncertainties. The proposed algorithm integrated the advantages of the response surface method (RSM), finite element method (FEM) and Monte Carlo simulation (MCS). Uncertainties in the structural parameters can be taken into account in this algorithm. The algorithm is verified using independently generated finite element data. The proposed algorithm is then used to analyze the shear-lag effects of a simply supported beam with parameter uncertainties. The results show that the proposed algorithm based on the central composite design is the most promising one in view of its accuracy and efficiency. Finally, a parametric study was conducted to investigate the effect of each of the random variables on the statistical moment of structural stress response.