In this proof-of-concept study, we questioned whether the influence of TMS on cortical excitability can be applied to classical conditioning. More specifically, we investigated whether the faciliatory influence of paired-pulse TMS on the excitability of the human motor cortex can be transferred to a simultaneously presented auditory stimulus through conditioning. During the conditioning phase, 75 healthy young participants received 170 faciliatory paired TMS pulses (1st pulse at 95% resting motor threshold, 2nd at 130%, interstimulus interval 12 ms), always presented simultaneously with one out of two acoustic stimuli. In the test phase, 20 min later, we pseudorandomly applied 100 single TMS pulses (at 130% MT), 50 paired with the conditioned tone—50 paired with a control tone. Using the Wilcoxon-Signed Rank test, we found significantly enhanced median amplitudes of motor evoked potentials (MEPs) paired with the conditioned tone as compared to the control tone, suggesting successful conditioning (p = 0.031, responder rate 55%, small effect size of r = − 0.248). The same comparison in only those participants with a paired-pulse amplitude < 2 mV in the conditioning phase, increased the responder rate to 61% (n = 38) and effect size to moderate (r = − 0.389). If we considered only those participants with a median paired-pulse amplitude < 1 mV, responder rate increased further to 79% (n = 14) and effect size to r = − 0.727 (i.e., large effect). These findings suggest increasingly stronger conditioning effects for smaller MEP amplitudes during paired-pulse TMS conditioning. These proof-of-concept findings extend the scope of classical conditioning to faciliatory paired-pulse TMS.