Transcranial magnetic stimulation (TMS) is a non-invasive method allowing both investigating and modulating human brain in normal and pathological conditions. One of the most serious problems limiting TMS use in research and clinical practice is the high variability of its effects. In recent years, it became widely accepted that the effects of TMS protocols is not just a property of a TMS protocol itself, but a consequence of the interactions of the intervention with the individual neuronal phenotype and ongoing functional state, which is primarily based on the ongoing neuronal activity. Thus, it is necessary to develop TMS approaches that take into account the ongoing neuronal activity, the so-called state/activity-dependent TMS. Here we present software that allows considering both the position of the magnetic stimulator and the ongoing biological activity for the purpose of TMS triggering. The software allows automatic TMS triggering when several conditions are met: the beginning of the movement/activation of a target muscle, lack of the preactivation of a non-target muscle and a correct positioning of a magnetic coil. The novelty of the developed neuronavigation software is due to a combination of spatial information about the position of a magnetic coil ("where?") and temporal information about the ongoing biological activity ("when?"). The time lag for the stimulation triggering was tested in an experiment with TMS triggered by a movement onset; and it was about 20 ms. Further software development is planned towards the introduction of EEG-dependent TMS approaches. The latency for TMS triggering was tested in an experiment with TMS triggered by a movement onset. In the future implementation of EEG-based TMS approaches is planned. We believe that the development of such a technical solution for neuronavigated activity-dependent TMS is important to bring TMS methodology to a new level of the spatio-temporal specificity.