Background: Exercise has been shown to alter brain plasticity and is explored as a therapeutic intervention in a wide variety of neurological diseases. Electroencephalography (EEG) offers an inexpensive method of studying brain electrocortical activity shortly after exercise and thus offers a way of exploring the influence of exercise on the brain. We conducted a systematic review to summarize the current body of evidence regarding methods of EEG analysis and the reported effects of exercise interventions on EEG. Methods: PubMed, Web of Science and EMBASE were searched for studies investigating resting state EEG in exercise intervention studies carried out in participants >17 years of age and with no history of epilepsy. Further, studies solely investigating event-related potentials as an outcome measure were excluded. Relevant data were extracted, and a risk-of-bias assessment was carried out using the Cochrane risk-of-bias tool. A qualitative synthesis of results was carried out. A protocol for the systematic review was uploaded to https://www.crd.york.ac.uk/PROSPERO/ (ID: CRD42019134570) and the Preferred Reporting Items for Systematic Reviews (PRISMA) statement was followed. Results: Out of 1,993 records screened, 54 studies were included in a final qualitative synthesis with a total of 1,445 participants. Our synthesis showed that studies were mainly carried out using frequency analysis as an analytical method. Generally, findings across studies were inconsistent and few were adjusted for multiple comparisons. Studies were mainly of low quality and usually carried out in small populations, lowering the significance of results reported. Conclusions: Changes in the EEG as a result of an exercise intervention are elusive and difficult to replicate. Future studies should provide biologically sound hypotheses underlying assumptions, include larger populations and use standardized EEG methods to increase replicability. EEG remains an interesting methodology to examine the effects of exercise on the brain.