Transcranial magnetic stimulation (TMS)‐evoked potentials (TEPs) are a promising proxy for measuring effective connectivity, that is, the directed transmission of physiological signals along cortico‐cortical tracts, and for developing connectivity‐based biomarkers. A crucial point is how stimulation parameters may affect TEPs, as they may contribute to the general variability of findings across studies. Here, we manipulated two TMS parameters (i.e. current direction and pulse waveform) while measuring (a) an early TEP component reflecting contralateral inhibition of motor areas, namely, M1‐P15, as an operative model of interhemispheric cortico‐cortical connectivity, and (b) motor‐evoked potentials (MEP) for the corticospinal pathway. Our results showed that these two TMS parameters are crucial to evoke the M1‐P15, influencing its amplitude, latency, and replicability. Specifically, (a) M1‐P15 amplitude was strongly affected by current direction in monophasic stimulation; (b) M1‐P15 latency was significantly modulated by current direction for monophasic and biphasic pulses. The replicability of M1‐P15 was substantial for the same stimulation condition. At the same time, it was poor when stimulation parameters were changed, suggesting that these factors must be controlled to obtain stable single‐subject measures. Finally, MEP latency was modulated by current direction, whereas non‐statistically significant changes were evident for amplitude. Overall, our study highlights the importance of TMS parameters for early TEP responses recording and suggests controlling their impact in developing connectivity biomarkers from TEPs. Moreover, these results point out that the excitability of the corticospinal tract, which is commonly used as a reference to set TMS intensity, may not correspond to the excitability of cortico‐cortical pathways.