This is the first case description of primary amebic meningoencephalitis (PAM) in an Iranian child. The patient was an eighteen months old boy referred to the hospital with signs and symptoms of acute meningitis. Cerebrospinal fluid (CSF) examination indicated pleocytosis with predominance of neutrophils, low sugar and high protein. Gram staining and culture of CSF for bacteria were negative. Microscopic examination of CSF revealed the motile amebae with pseudopodia. In Giemsa staining of CSF, the trophzoites of amebae were observed. The initial response to a six-week treatment course with amphotericin B, rifampin and chloramphenicol was satisfactory, but in the follow-ups the patient regressed neurologically. Although PAM is a rare and fatal disease, it should be differentiated from bacterial meningitis and treatment must be promptly carried out.