The scaled boundary finite element method (SBFEM) is a semi-analytical computational method initially developed in the 1990s. It has been widely applied in the fields of solid mechanics, oceanic, geotechnical, hydraulic, electromagnetic and acoustic engineering problems. Most of the published work on SBFEM has focused on its theoretical development and practical applications, but, so far, no explicit discussion on the numerical stability and accuracy of its solution has been systematically documented. However, for a reliable engineering application, the inherent numerical problems associated with SBFEM solution procedures require thorough analysis in terms of its causes and the corresponding remedies. This study investigates the numerical performance of SBFEM with respect to matrix manipulation techniques and their properties. Some illustrative examples are given to identify reasons for possible numerical difficulties, and corresponding solution schemes are proposed to overcome these problems.