To assess the clinical significance of repeated head imaging in children with minor blunt force head trauma who underwent computed tomography (CT), limited to those who exclude with very low risk of important traumatic brain injury. We conducted a retrospective cohort study of children aged under 24 months with minor head trauma who underwent repeated head imaging and initial CT scans according to the Pediatric Emergency Care Applied Research Network (PECARN) rules. We enrolled 741 children and 110 with skull fracture (SF). Of the 96 patients with SF on initial CT who received head magnetic resonance imaging (MRI) a few days later, 36 (37.5%) patients' initial CT findings revealed intracranial injury in addition to SF. The number of children who exhibited new intracranial findings on follow-up MRI among those with isolated SF without intracranial damage and those with SF and intracranial injury on initial CT was 25/60 (40.7%) and 14/36 (38.9%), respectively. Subcutaneous hematoma on arrival and intersection with the coronal suture and lines of fracture were significantly associated with new intracranial findings. Four children with SF and intracranial injury on initial CT received neurosurgical intervention. No intervention was needed for those with isolated SF. We demonstrated that a proportion of children with head trauma had new findings on follow-up MRI, particularly in those without very low risk of clinically important traumatic brain injury. Patients who exhibit new intracranial MRI findings that satisfy the PECARN rules may not require neurosurgical intervention if their initial CT finding is isolated SF.