Abstract Volume conductor models of the human head are routinely used to estimate the induced electric fields in transcranial brain stimulation (TBS) and for source localization in electro- and magnetoencephalography (EEG and MEG). Magnetic resonance current density imaging (MRCDI) has the potential to act as a non-invasive method for dose control and model validation but requires very sensitive MRI acquisition approaches. A double-echo echo-planar imaging (EPI) method is here introduced. It combines fast and sensitive imaging of the magnetic fields generated by the current flow of transcranial electric stimulation with increased robustness to physiological noise. For validation, noise floor measurements without injected currents were obtained in five subjects for an established multi-echo gradient-echo (MGRE) sequence and the new EPI method. In addition, data with current injection were acquired in each subject with a right-left (RL) and anterior-posterior (AP) electrode montage with both sequences to assess the accuracy of subject-specific detailed head models. In line with previous findings, the noise floor measurements showed that the MGRE results suffered from spatial low-frequency noise patterns, which were mostly absent in the EPI data. A recently published approach optimizes the ohmic conductivities of subject-specific head models by minimizing the difference between simulated and measured current-induced magnetic fields. Here, simulations demonstrated that the MGRE noise patterns have a larger negative impact on the optimization results than the EPI noise. For the current injection measurements, a larger discrepancy was found for the RL electrode montage compared with the AP electrode montage consistently for all subjects. This discrepancy that remained in part also after optimization of the ohmic conductivities, was similar for the data of the two sequences and larger than the measurement noise, and thus demonstrates systematic biases in the volume conductor models. We have shown that EPI-based MRCDI is superior to established techniques by mitigating the effects of previously reported spatial low-frequency noise in MRCDI if limited spatial resolution is acceptable. Additionally, the consistent inter-subject results indicate that MRCDI is capable of picking up inaccuracies in computational head models and will be useful to guide systematic improvements.