In recent years, there has been a heightened interest in the effect of non-invasive brain stimulation on executive functioning. However, there is no comprehensive overview of its effects on different executive functioning domains in healthy individuals. Here, we assessed the state of the field by conducting a systematic review and meta-analysis on the effectiveness of non-invasive brain stimulation (i.e. repetitive transcranial magnetic stimulation and transcranial direct current stimulation) over prefrontal regions on tasks assessing working memory, inhibition, flexibility, planning and initiation performance. Our search yielded 63 studies (n = 1537), and the effectiveness of excitatory and inhibitory non-invasive brain stimulation were assessed per executive functioning task. Our analyses showed that excitatory non-invasive brain stimulation had a small but positive effect on Stop Signal Task and Go/No-Go Task performance, and that inhibitory stimulation had a small negative effect on Flanker Task performance. Non-invasive brain stimulation did not affect performance on working memory and flexibility tasks, and effects on planning tasks were inconclusive.