Recognizing and identifying dysautonomia would facilitate the diagnosis and management of MECP2 mutations in boys. We aimed to explore the prevalence of dysautonomia symptoms in boys with MECP2 mutations. We conducted a national, retrospective study (2000-2020) of medical records from boys who were aged less than 18 years when diagnosed with a pathogenic, or likely pathogenic, variant in the MECP2 gene. We systematically looked for dysautonomic signs in the cardiovascular, respiratory, gastrointestinal, and thermoregulatory systems. Nine of the 13 cases had at least one system affected by dysautonomia. Two patient subgroups were identified: (1) patients who were ambulatory with intellectual or learning disabilities (n = 6/13 cases) and (2) patients who were unable to walk normally with severe encephalopathy (n = 7/13 cases). Dysautonomic signs were found in both subgroups: 7 of seven patients in the severe array subgroup and 2 of six in the mild array subgroup. These results support MECP2 testing and dysautonomia investigations in both young males who present with encephalopathy and those with intellectual disabilities.