Juvenile myoclonic epilepsy (JME) has been classified as a syndrome of idiopathic generalized epilepsy and is characterized by a strong genetic basis, age-specific onset of seizures, specific types of seizures, generalized spike-wave discharges on electroencephalography, and a lack of focal abnormality on magnetic resonance imaging (MRI). Recently, a wide range of advanced neuroimaging techniques have been utilized to elucidate the neuroanatomical substrates and pathophysiological mechanisms underlying JME. Specifically, a number of quantitative MRI studies have reported focal or regional abnormalities of the subcortical and cortical grey matter, particularly the thalamus and frontal cortex, in JME patients. In addition, diffusion tensor imaging studies have pointed to disrupted microstructural integrity of the corpus callosum and multiple frontal white matter tracts as well as thalamofrontal dysconnectivity in JME patients. Converging evidence from neuroimaging studies strongly suggests that JME is a predominantly thalamofrontal network epilepsy, challenging the traditional concept of JME as a generalized epilepsy. There is also limited evidence indicating extrafrontal and extrathalamic involvement in JME. This systematic review outlines the main findings from currently available MRI studies focusing on grey and white matter alterations, and discusses their contributions to the etiology and pathophysiology of JME. The clinical utility, advantages, and drawbacks of each imaging modality are briefly described as well.