The study of the metaplasticity-based transcranial magnetic stimulation (TMS) protocols is an extensively studied approach to increase the effectiveness of stimulation. However, the effects of protocols with different intervals between the TMS blocks on cognitive functions are poorly understood. The study was aimed to assess the effects of two theta-burst transcranial stimulation (iTBS) protocols with short and long intervals between blocks on the working memory (WM) performance in healthy volunteers. A total of 16 participants were underwent a single TMS session of each protocol, which were applied in random order (iTBS 0–15 — two iTBS blocks over the left dorsolateral prefrontal cortex (DLPFC) iTBS with an interval of 15 min between blocks followed by stimulation of the vertex area in 60 min after the first block; iTBS 0–60 — iTBS block over the left DLPFC iTBS, block of the vertex stimulation after 15 min, and the second block of iTBS over the left DLPFC iTBS 60 min after the first one; iTBS 0 — one block of iTBS over the left DLPFC iTBS and two blocks of the vertex stimulation; control protocol — three blocks of the vertex stimulation with similar intervals). WM was assessed using the n-back test before the first block and after the second and the third stimulation blocks. No significant effects of protocols on  WM or differences between protocols in alterations of test results and the responder rates to TMS between protocols were observed. The trend toward statistical signficance was reported for the protocol with short interval (iTBS 0–15). Furthermore, low reproducibility of individual iTBS effect was reported. The study of protocols with short intervals between blocks involving larger cohort of volunteers and taking into account the other factors potentially influencing the effect of the protocol (number of blocks and duration of a single block) seems to be promising.