Background Magnetic resonance imaging (MRI) of the brain in children and adolescents is a well-established method in both clinical practice and in neuroscientific research. This practice is sometimes viewed critically, as MRI scans might expose minors (e.g. through scan-associated fears) to more than the legally permissible "minimal burden". While there is evidence that a significant portion of adults undergoing brain MRI scans experience anxiety, data on anxiety in children and adolescents undergoing brain MRI scans is rare. This study therefore aimed to examine the prevalence and level of anxiety in children and adolescents who had MRI scans of the brain, and to compare the results to adults undergoing brain MRI scans, and to children and adolescents undergoing electroencephalography (EEG; which is usually regarded a "minimal burden"). Method Participants were 57 children and adolescents who had a brain MRI scan (MRI-C; mean age 12.9 years), 28 adults who had a brain MRI scan (MRI-A; mean age 43.7 years), and 66 children and adolescents undergoing EEG (EEG-C; mean age 12.9 years). Anxiety was assessed on the subjective (situational anxiety) and on the physiological level (arousal), before and after the respective examination. Results More than 98% of children and adolescents reported no or only minimal fear during the MRI scan. Both pre-and post-examination, the MRI-C and the MRI-A groups did not differ significantly with respect to situational anxiety (p = 0.262 and p = 0.374, respectively), and to physiological arousal (p = 0.050, p = 0.472). Between the MRI-C and the EEG-C group, there were also no significant differences in terms of situational anxiety (p = 0.525, p = 0.875), or physiological arousal (p = 0.535, p = 0.189). Prior MRI experience did not significantly influence subjective or physiological anxiety parameters. Conclusions In this study, children and adolescents undergoing a brain MRI scan did not experience significantly more anxiety than those undergoing an EEG, or adults undergoing MRI scanning. Therefore, a general exclusion of minors from MRI research studies does not appear reasonable.