Overlay restorations are a conservative option for restoring molars while preserving tooth structure. Lithium disilicate and milled composite have biomechanical differences that can influence stress distribution and strength of the restored tooth. Finite element analysis (FEA) allows the evaluation of these effects under functional loading conditions. Objective: To compare the stress and strain distribution in lithium disilicate and milled composite overlay restorations by means of finite element analysis. Material and methods: Three-dimensional models of mandibular molars restored with 2 mm thick overlays in lithium disilicate, and milled composite were generated, as well as a control group. An axial load of 300 N was applied at five occlusal contact points and the Von Mises stress and maximum deformation at the restoration-tooth structure interface were analyzed. Results: Lithium disilicate showed the highest Von Mises stresses (75.9 MPa) and the least deformation (0.0152 mm), while the milled composite showed lower stresses (60.2 MPa) and higher deformation (0.0307 mm). The intact tooth showed the lowest stress values (45.3 MPa) with an intermediate strain (0.0225 mm). Conclusion: Lithium disilicate presents higher strength but transfers more stresses to the tooth root, while the milled composite absorbs better the occlusal loads but with higher deformation. These results can guide the selection of materials in indirect restorations according to the biomechanical needs of the patient.