Purpose. The development of a wide construction market and a desire to design innovative architectural building constructions has resulted in the need to create complex numerical models of objects having increasingly higher computational complexity. The purpose of this work is to show that choosing a proper method for solving the set of equations can improve the calculation time (reduce the complexity) by a few levels of magnitude. Methodology. The article presents an analysis of the impact of matrix inversion algorithm on the deflection calculation in the beam, using the finite element method (FEM). Based on the literature analysis, common methods of calculating set of equations were determined. From the found solutions the Gaussian elimination, LU and Cholesky decomposition methods have been implemented to determine the effect of the matrix inversion algorithm used for solving the equations set on the number of computational operations performed. In addition, each of the implemented method has been further optimized thereby reducing the number of necessary arithmetic operations. Findings. These optimizations have been performed on the use of certain properties of the matrix, such as symmetry or significant number of zero elements in the matrix. The results of the analysis are presented for the division of the beam to 5, 50, 100 and 200 nodes, for which the deflection has been calculated. Originality. The main achievement of this work is that it shows the impact of the used methodology on the complexity of solving the problem (or equivalently, time needed to obtain results). Practical value. The difference between the best (the less complex) and the worst (the most complex) is in the row of few orders of magnitude. This result shows that choosing wrong methodology may enlarge time needed to perform calculation significantly.