Combining Non-Invasive Brain Stimulation (NIBS) techniques with the recording of brain electrophysiological activity is an increasingly widespread approach in neuroscience. Particularly successful has been the simultaneous combination of Transcranial Magnetic Stimulation (TMS) and Electroencephalography (EEG). Unfortunately, the strong magnetic pulse required to effectively interact with brain activity inevitably induces artifacts in the concurrent EEG acquisition. Therefore, a careful but aggressive pre-processing is required to efficiently remove artifacts. Unfortunately, as already reported in the literature, different preprocessing approaches can introduce variability in the results. Here we aim at characterizing the three main TMS-EEG preprocessing pipelines currently available, namely ARTIST (Wu et al., 2018), TESA (Rogasch et al., 2017) and SOUND/SSP-SIR (Mutanen et al., 2018, 2016), providing an insight to researchers who need to choose between different approaches. Differently from previous works, we tested the pipelines using a synthetic TMS-EEG signal with a known ground-truth (the artifacts-free to-be-reconstructed signal). In this way, it was possible to assess the reliability of each pipeline precisely and quantitatively, providing a more robust reference for future research. In summary, we found that all pipelines performed well, but with differences in terms of the spatio-temporal precision of the ground-truth reconstruction. Crucially, the three pipelines impacted differently on the inter-trial variability, with ARTIST introducing inter-trial variability not already intrinsic to the ground-truth signal.