In the present study the problem of calculation of the stress intensity factors (SIFs) of semi-elliptical cracks located in the stress concentration areas of an expansion joint (EJ) situated between the lower barrel and the upper barrel of a pressure vessel research reactors (RRs) is numerically solved by advanced global-local finite element (FE) analysis. The common characteristic of the cases solved is that the stress field at the crack area varies along the axial, the circumferential, as well as, the through-the-thickness directions. SIF solutions for such problems are not available, neither analytically, nor numerically, as the currently existing solutions in the literature (numerical results, Newman–Raju empirical equations, weight function solutions, etc.) are only valid for uniform stress distribution along the axial and circumferential directions of the pressure vessel and allow variation only through-the-thickness. The crack locations considered are the intersection of the various parts that constitute the EJ and the connection of the EJ with the lower barrel. The stress intensity factors are presented in a suitable table format for various geometrical configurations of the semi-elliptical crack and of both the variation of a/c and a/t, thus providing a useful tool for the fracture mechanics design of cracked EJ. The modeling details of the methodology, employed in the analysis, are extensively discussed and the numerical approach is proven to be very efficient for the SIFs calculation of EJ semi-elliptical cracks.