The impact of the deep margin elevation (DME) technique and its associated materials on the stress distribution in ceramic endocrowns remains to be fully understood. This finite element analysis (FEA) aimed to assess the effects of flowable composite and resin-modified glass ionomer (RMGI) as DME materials on the maximum Von Mises stress (VMS) values and overall stress distribution within ceramic endocrowns and the surrounding tooth structure. A mandibular molar featuring a class II mesio occlusal (MO) cavity with the gingival margin of the mesial cavity positioned 2 mm below the cementoenamel junction (CEJ) was prepared and scanned using a Medit i500 scanner. The digital file was then transferred to computer-aided design (CAD) software to create the models. The study generated four scenarios: an intact tooth model (model of intact tooth (MIT)), a prepared tooth model without a DME layer (model without DME (MWD)), a model with a 2 mm DME layer using composite material (model with DME of composite (MDC)), and a model employing RMGI (model with DME of RMGI (MDR)). Stress distribution under axial loads was evaluated based on the Von Mises criterion. The MIT model demonstrated the highest stress concentration at the CEJ region yet exhibited lower stress levels than others. The MWD model showed the highest stress levels. No significant differences in stress distribution patterns were observed between the MDR and MDC models. All models displayed similar stress distributions in the bone. Regardless of the material used, incorporating a DME layer in cavities extending below the CEJ is advisable to achieve uniform stress distribution. Minimizing tooth preparation and preserving tooth structure are recommended. Employing a DME layer in cavities with margins below the CEJ is beneficial for reducing stress, irrespective of the material choice.