The EEG acquired simultaneously with fMRI is distorted by a number of artefacts related to the presence of strong magnetic fields, which must be reduced in order to allow for a useful interpretation and quantification of the EEG data. For the two most prominent artefacts, associated with magnetic field gradient switching and the heart beat, reduction methods have been developed and applied successfully. However, a number of artefacts related to the MR-environment can be found to distort the EEG data acquired even without ongoing fMRI acquisition. In this paper, we investigate the most prominent of those artefacts, caused by the Helium cooling pump, and propose a method for its reduction and respective validation in data collected from epilepsy patients. Since the Helium cooling pump artefact was found to be repetitive, an average template subtraction method was developed for its reduction with appropriate adjustments for minimizing the degradation of the physiological part of the signal. The new methodology was validated in a group of 15 EEG–fMRI datasets collected from six consecutive epilepsy patients, where it successfully reduced the amplitude of the artefact spectral peaks by 95 ± 2 % while the background spectral amplitude within those peaks was reduced by only −5 ± 4 %. Although the Helium cooling pump should ideally be switched off during simultaneous EEG–fMRI acquisitions, we have shown here that in cases where this is not possible the associated artefact can be effectively reduced in post processing.