Magnetic resonance imaging (MRI) procedures often evoke anxiety in children. Further, anxious children may be less likely to participate in MRI research, leading to a possible selection bias, and may be more likely to move during image acquisition, resulting in lower image quality and possible information bias. Therefore, state anxiety is problematic for functional and structural MRI studies. Children with behavioral problems, such as internalizing and externalizing behaviors, may be more likely to experience state anxiety prior to and during MRI scanning. Therefore, our first aim was to investigate the relationship between internalizing/externalizing behavior and children’s MRI-related state anxiety. Our second aim was to investigate the relationship between internalizing and externalizing behaviors and MRI research participation. Our final aim was to investigate the effect of internalizing and externalizing behaviors as well as MRI-related anxiety on image quality in children. We included 1,241 six- to ten-year-old children who underwent a mock MRI. Afterward, if not too anxious, these children were scanned using a 3-Tesla GE Discovery MRI system (n = 1,070). Internalizing and externalizing behaviors were assessed with the child behavior checklist. State anxiety was assessed with a visual analog scale. Internalizing behaviors were positively associated with child state anxiety, as reported by the child, parent, and researcher. For state anxiety reported by the parent and researcher, this relationship was independent of externalizing behaviors. Externalizing behaviors were related to state anxiety as reported by the child, parent, and researcher, but this difference was not independent of internalizing behaviors, pointing toward a relationship via the shared variance with internalizing behaviors. Further, children with more internalizing and externalizing behaviors were less likely to participate in the actual MRI-scanning procedure. Lastly, MRI-related state anxiety, reported by the child and the researcher, was associated with worse image quality. These results underscore the potential for biases and methodological issues related to MRI-related state anxiety in children.