Background: Tuberous sclerosis complex (TSC) is a rare autosomal dominant hereditary neurodermal syndrome with diverse clinical manifestations, implicating multiple organs including the nervous system, skin, kidney, lung, heart, eyes and others. Most of the children are first diagnosed with seizures or facial hemangiofibroma, 45% to 60% of patients with TSC lesions can affect the heart resulting in cardiac rhabdomyoma. Although most cardiac rhabdomyomas are asymptomatic, some children may develop severe symptoms such as hemodynamic abnormalities, arrhythmias, and even heart failure in the neonatal period and early infancy. But Tuberous sclerosis complex with apical hypertrophic cardiomyopathy as the first manifestation is rare. Hence, physicians may delay diagnosis and treatment of TSC due to the lack of comprehensive thinking on this atypical presentation.Case presentation A 5-year-old girl was admitted to our hospital due to syncope for more than 10 days. When she was 8 months old, she was diagnosed with hypertrophic cardiomyopathy and received long-term oral propranolol treatment. After her admission, a thorough examination was performed. Heart exam revealed the revelant problem. Brain MRI demonstrated mutiple nodules in bilateral frontal parietal occipital cortex, subcortical cortex and bilateral lateral ventricular margin consistent with TSC. Genetic analysis (high-precision clinical display PLUS, JiaJian Medicine Company) revealed that the patient had inherited the TSC2 mutation c.1343T> C (p.L448P) from her mother (heterozygous), who was clinically unaffected.Conclusions: This report highlights that TSC occurs in different ways. Given the possibility of insidious and atypical tuberous sclerosis, when apical hypertrophy or cardiac tumors are identified, it is recommended to broaden the systemic examination even including genetic testing to further determine the cause, in order to reduce the misdiagnosis rate of tuberous sclerosis.