Magnetic resonance elastography (MRE) is a noninvasive method for mapping brain stiffness. Ultrasound-based transtemporal time-harmonic elastography (THE) is emerging as a cost-effective, fast alternative to MRE that has the potential to be used for bedside monitoring of intracranial pressure. We aim to investigate the accuracy of THE in direct comparison with MRE performed in the brain. Ten healthy volunteers (25–40 years old) successively underwent multifrequency MRE (20 Hz − 35 Hz) and THE (27 Hz − 56 Hz) of the brain. Fiducial-marker-based optical tracking of the ultrasound field of view was used to align THE to 3D MRE. THE- and MRE-derived shear wave speed (SWS) was determined as a measure of brain stiffness and averaged within different brain regions of various depths for cross-modality correlation analysis. MRE-measured SWS in temporal lobe regions ranged from 1.0 to 1.3 m/s and was negatively correlated with age (R2 = 0.44, p = 0.035). After registration of both modalities, there was linear correlation of SWS values (MRE: 1.14 ± 0.08 m/s, THE: 1.13 ± 0.10 m/s; R2 = 0.62, p = 0.007). Best agreement between MRE and THE was achieved at depths of 40 to 50 mm, suggesting this range provides a viable trade-off between ultrasound attenuation and near-field bias. Similar brain regions can be consistently measured with both elastography modalities, despite the regional and individual variations of stiffness, and provided that similar stimulation frequencies are used. Cost-effective and fast transtemporal THE yields stiffness values of the temporal lobe in a range similar to those obtained with more expensive MRE.