Due to improved medical techniques such as CT and radiotherapy todays children are more exposed to low-dose radiation than previous generations. However, little is known about the influence of low-dose radiation on the brain’s development. We hypothesize that altered functional connectivity of activated areas during pain processing can serve as a marker for disturbed brain development. In a mouse model we showed that functional connectivity during nociceptive stimulation after P10 irradiation is disrupted in cortical areas that mature postnatal. We could demonstrate that pain processing is influenced by low-dose irradiation which is in concordance with the brain’s developmental state.