The understanding of the lateral variations in the lithospheric strength can help in identifying the distribution pattern of surface deformation and its response to long-term forces that are related to deep Earth processes. Former studies suggest that Afar and the Ethiopian Plateaus are not in isostatic equilibrium indicating the presence of deep compensation processes. We estimated the effective elastic thickness of the lithosphere (Te) over Ethiopia and its surrounding region using a method that combines the Vening Meinesz-Mortiz and flexural theory of isostasy in a spherical harmonics domain. Our effective elastic thickness model is different from those presented in the previous similar studies, because of considering the effects of mantle dynamics. We incorporated the uplift forces due to mantle plume in additions to surface and sub-surfaces loads, like topographic/bathymetric masses, crustal crystalline and sediments in our method so that it becomes more appropriate for the regions. In addition, laterally-variable models of upper mantle density, Young’s modulus and Poisson’s ratio have been considered from the CRUST1.0 model. We found a significant improvement of the solution in the Te estimate with consideration of the dynamic effects when we compared it with other studies especially in Afar, the Ethiopian plateaus, and the Main Ethiopian Rift valley. Our results are also consistent with significant lithospheric strength present in cratonic formations, with maximum of Te in Sudan and Tanzanian Cratons. Low Te was found over different tectonically active places such as, Afar and the Main Ethiopian Rift valley.