Realistic computer simulation of neurosurgical procedures requires incorporation of the mechanical properties of brain tissue in the mathematical model. Possible applications of computer simulation of neurosurgery include non-rigid registration, virtual reality training and operation planning systems and robotic devices to perform minimally invasive brain surgery. A number of constitutive models of brain tissue, both single-phase and bi-phasic, have been proposed in recent years. The major deficiency of most of them, however, is the fact that they were identified using experimental data obtained in vitro and there is no certainty whether they can be applied in the realistic in vivo setting. In this paper we attempt to show that previously proposed by us hyper-viscoelastic constitutive model of brain tissue can be applied to simulating surgical procedures. An in vivo indentation experiment is described. The force–displacement curve for the loading speed typical for surgical procedures is concave upward containing no linear portion from which a meaningful elastic modulus might be determined. In order to properly analyse experimental data, a three-dimensional, non-linear finite element model of the brain was developed. Magnetic resonance imaging techniques were used to obtain geometric information needed for the model. The shape of the force–displacement curve obtained using the numerical solution was very similar to the experimental one. The predicted forces were about 31% lower than those recorded during the experiment. Having in mind that the coefficients in the model had been identified based on experimental data obtained in vitro, and large variability of mechanical properties of biological tissues, such agreement can be considered as very good. By appropriately increasing material parameters describing instantaneous stiffness of the tissue one is able, without changing the structure of the model, to reproduce experimental curve almost perfectly. Numerical studies showed also that the linear, viscoelastic model of brain tissue is not appropriate for the modelling brain tissue deformation even for moderate strains.