Minor head trauma (MHT) is very frequent in children and post-traumatic headache (PTH) is one of its most common complications; however, its management is still a challenge. We aimed to assess the incidence and clinical characteristics of, and risk factors for, PTH among children referred to our pediatric emergency department (PED) for MHT. A total of 193 patients aged 3–14 years evaluated for MTH were enrolled and followed up for 6 months through phone calls and/or visits. PTH occurred in 25/193 patients (13%). PTH prevalence was significantly higher in school-aged (≥6 years) than in pre-school-aged children (21.6% vs. 4.9%, respectively, p < 0.009). Females were found to be more affected. The median time of onset was 4.6 days after MHT; resolution occurred in a median of 7 weeks. In 83.3% of patients, PTH subsided in <3 months, while in 16.7% it persisted longer. A total of 25% of children exhibited the migraine and 75% the tension-type variant. Our analysis indicates the presence of headache upon arrival in PED, isolated or associated with nausea and dizziness, as a factor predisposing the patient to the development of PTH. Our findings could be useful to identify children at risk for PTH for specific follow-up, family counseling, and treatment.