Electron beam welding (EBW) is one of the most highly precise methods that is gaining more importance in high-strength structural steel (HSSS) thicker plate application in various vehicles, construction industries, etc. Since it offers particular advantages over arc welding processes like narrow welds, reduced heat-affected zone (HAZ), and low distortion, it inherits lower linear heat input characteristics. The main purpose of this study is to analyze and compare the effect of localized electron beam–post-weld heat treatment (LEB-PWHT) with that of an as-welded EB-welded S960QL joint of a thickness of 12 mm for various joint and HAZ properties. LEB-PWHT can be beneficial in terms of time saving, more local treatment, higher flexibility, energy saving, greater efficiency, increased productivity, etc. In this study, LEB-PWHT was applied to an autogenous EB-welded S960QL joint using a defocused beam. Microstructural characteristics were observed through light optical and scanning electron microscopy (SEM) while mechanical properties, including microhardness, tensile strength, bending, and Charpy V-notch (CVN) impact test, are compared in as-welded and LEB-PWHT joints. The microstructural results showed that the EBW coarse-grain heat-affected zone (CGHAZ) consists of martensite, while the PWHT weld metal contains tempered martensite with carbide precipitates. The fine-grain heat-affected zone (FGHAZ) of EBW exhibits a martensitic and bainitic microstructure, whereas the FGHAZ of the PWHT joint exhibits equiaxed grain with finely dispersed carbides. The hardness decrease after LEB-PWHT in the weld metal and HAZ was approximately 23% and 21%, respectively. An increase in tensile strength (3%) was observed in the LEB-PWHT joints (1082 MPa) compared to the EBW joint (1051 MPa). Both tensile and bending tests demonstrated improved ductility behavior after PWHT. However, the impact test at −40 °C indicated a reduction in toughness in the weld metal of LEB-PWHT (27 J) compared to EBW (63 J).