Theta-burst stimulation (TBS) can be a non-invasive technique to modulate cognitive functions, with promising therapeutic potential, but with some contradictory results. Event related potentials are used as a marker of brain deterioration and can be used to evaluate TBS-related cognitive performance, but its use remains scant. This study aimed to study bilateral inhibitory and excitatory TBS effects upon neurocognitive performance of young healthy volunteers, using the auditory P300' results. Using a double-blind sham-controlled study, 51 healthy volunteers were randomly assigned to five different groups, two submitted to either excitatory (iTBS) or inhibitory (cTBS) stimulation over the left dorsolateral pre-frontal cortex (DLPFC), two other actively stimulated the right DLPFC and finally a sham stimulation group. An oddball based auditory P300 was performed just before a single session of iTBS, cTBS or sham stimulation and repeated immediately after. P300 mean latency comparison between the pre- and post-TBS stimulation stages revealed significantly faster post stimulation latencies only when iTBS was performed on the left hemisphere (p = 0.003). Right and left hemisphere cTBS significantly delayed P300 latency (right p = 0.026; left p = 0.000). Multiple comparisons for N200 showed slower latencies after iTBS over the right hemisphere. No significant difference was found in amplitude variation. TBS appears to effectively influence neural networking involved in P300 formation, but effects seem distinct for iTBS vs cTBS and for the right or the left hemisphere. P300 evoked potentials can be an effective and practical tool to evaluate transcranial magnetic stimulation related outcomes.