Background Although the relationship between neuronavigated transcranial magnetic stimulation (nTMS) and functional magnetic resonance imaging (fMRI) has been widely studied in motor mapping, it is unknown how the motor response type or the choice of motor task affect this relationship. New method Centers of gravity (CoGs) and response maxima were measured with blood-oxygen-level dependent (BOLD) and arterial spin labeling (ASL) fMRI during motor tasks against nTMS CoGs and response maxima, which were mapped with motor evoked potentials (MEPs) and silent periods (SPs). Results No differences in motor representations (CoGs and response maxima) were observed in lateral-medial direction (p = 0.265). fMRI methods localized the motor representation more posterior than nTMS (p < 0.001). This was not affected by the BOLD fMRI motor task (p > 0.999) nor nTMS response type (p > 0.999). ASL fMRI maxima did not differ from the nTMS nor BOLD fMRI CoGs (p ≥ 0.070), but the ASL CoG was deeper in comparison to other methods (p ≤ 0.042). The BOLD fMRI motor task did not influence the depth of the motor representation (p ≥ 0.745). The median Euclidean distances between the nTMS and fMRI motor representations varied between 7.7 mm and 14.5 mm and did not differ between the methods (F ≤ 1.23, p ≥ 0.318). Comparison with existing methods The relationship between fMRI and nTMS mapped excitatory (MEP) and inhibitory (SP) responses, and whether the choice of motor task affects this relationship, have not been studied before. Conclusions The congruence between fMRI and nTMS is good. The choice of nTMS motor response type nor BOLD fMRI motor task had no effect on this relationship.