In order for fMRI findings to be valid and replicable, they must first adhere to quality standardisation. Currently, fMRI literature investigating idiopathic generalised epilepsy is heterogeneous in terms of design, acquisition, processing, and analysis. The present study reported the quality, methods, and functional connectivity findings of fMRI research investigating idiopathic generalised epilepsies, targeting studies that best represent valid and replicable methodologies. Twenty-four studies were identified in the present systematic review. The default mode network showed more significantly altered connectivity than other resting state networks. These networks and associated regions of interest were frequently deactivated at rest amongst all idiopathic generalised epilepsy subtypes compared to controls. This review highlights the need for standardization in acquisition techniques and parameters, processing steps, and analysis techniques, if research in this field is to be replicable. There is also a need for further investigation into default mode network connectivity in the juvenile absence epilepsy population, as a common subtype of idiopathic generalized epilepsy.