Neurofibromatosis type I (NF1) is an autosomal dominant disease. Some NF1 patients experience atypical clinical manifestations, genetic testing is not widely available, and the types of mutations vary; thus, they are prone to misdiagnosis and missed diagnosis. Although headache is not included in the diagnostic criteria for NF1, the incidence of headache in NF1 patients is not low. We report an NF1 family in which the proband presented with prominent headache and atypical clinical presentation, with limited skin pigmentation. We identified a frameshift mutation (c.1541_1542del, p. Q514Rfs*) in the NF1 gene by whole-exome sequencing of this family, and the patients were diagnosed with NF1. We hope to attract the attention of clinicians to these patients and improve genetic testing as soon as possible to increase the diagnosis rate.