OBJECTIVETranscranial magnetic stimulation (TMS) is extensively used in basic and clinical neuroscience. Previous work has shown substantial residual variability in TMS effects even despite use of on-line visual feedback monitoring of coil position. Here, we aimed to evaluate if off-line denoising of variability induced by neuronavigated coil position and orientation deviations can enhance detection of TMS effects.\n\nMETHODSRetrospective modeling was used to denoise the impact of common neuronavigated coil position and rotation deviations during TMS experimental sessions on motor evoked potentials (MEP) to single pulse TMS.\n\nRESULTSNeuronavigated coil deviations explained approximately 44% of total MEP amplitude variability. Offline denoising led to a 136.71% improvement in the signal to noise ratio (SNR) of corticospinal excitability measurements. CONCLUSIONS: Offline modeling enhanced detection of TMS effects by removing variability introduced by neuronavigated coil deviations.\n\nSIGNIFICANCEThis approach could allow more accurate determination of TMS effects in cognitive and interventional neuroscience.\n\nHIGHLIGHTSO_LICoil deviations impact TMS effects despite use of on-line neuronavigation feedback.\nC_LIO_LIOffline denoising of coil deviation impacts on TMS effects significantly reduced variability at trial level.\nC_LIO_LIOffline denoising also significantly improved overall SNR of TMS effects.\nC_LI