The aim of this study was to evaluate the stresses within simulated roots with internal resorption cavities at the apical, middle and coronal root levels, after obturation with gutta-percha and/or MTA utilising finite element analysis (FEA). Mandibular premolar teeth with internal resorption cavities at different root levels were modelled. Models were restored with gutta-percha and/or MTA. An oblique force of 300 N was applied and stress evaluations were carried out. In the MTA-filled resorption models, the stresses were distributed more homogeneously than the gutta-percha filled models, and the stress concentrations were lower in the remaining dentinal tissues. If the whole root is considered, the fully gutta-percha-filled models generated the highest stress values. Differences between the fully MTA-filled models and hybrid techniques were present only in the apical resorption models. Both the MTA and combination of MTA and gutta-percha can be suggested for use in clinical practice, in cases of internal root resorption cavity obturation.