As an important social cognitive function, empathy can help people establish harmonious interpersonal relationship and better adapt to the real society. Previous studies have shown that the occurrence, development and recurrence of many neurological and psychiatric diseases are related to empathy deficit. By modulating cortical excitability, non-invasive brain stimulation techniques (transcranial magnetic stimulation and transcranial direct current stimulation) can regulate the individual’s level of empathy and alleviate the symptoms of empathy deficit. The available evidence from healthy populations shows that the activities of the medial prefrontal cortex, the primary motor cortex, the inferior frontal gyrus, the dorsolateral prefrontal cortex and the temporoparietal junction help improve cognitive empathy. The activities of the bilateral dorsolateral prefrontal cortex can also help to down-regulate the level of affective empathy, while the activities of the right temporoparietal junction can enhance self-representation and support the self-other discrimination during empathy. There is a small amount of clinical evidence suggest that enhancing the activities of the left dorsolateral prefrontal cortex and the medial prefrontal cortex can improve cognitive empathy in patients with psychiatric and neurodegenerative diseases, respectively. Future research should explore empathy intervention with different stimulus parameters and stimulus sites under a unified behavioral measurement, and further investigate the mechanism of non-invasive brain stimulation in improving empathy by integrating other neurophysiological techniques. The effects of individual differences on brain intervention should also be considered.