Hypothalamic hamartoma is reported to be associated with precocious puberty. Here, the authors present a seven-year-old girl whose onset of puberty occurred at the age of two. Under the impression of idiopathic precocious puberty, cyproterone acetate was initially tried. Since the effect of her medication was not satisfactory, it was discontinued at the age of five years and 11 months. However, rapid advance of bone age and vaginal spotting recurred after the withdrawal of treatment. She was re-evaluated at the age of six, and a magnetic resonance image (MRI) study of the head revealed a hypothalamic hamartoma. At that time, a long-acting analog of luteinizing hormone-releasing hormone (LHRHa), leuprolide acetate, was prescribed. Her secondary sex characteristics regressed and her hypothalamic-pituitary-gonad axis was suppressed after treatment. The clinical presentation, mechanism and treatment of precocious puberty caused by hypothalamic hamartomas are fully discussed in this report.