The complication of Menkes disease (MD) and gastroesophageal reflux disease (GERD) is extremely rare. This report describes the very rare case of a one-year-old boy with MD complicated with GERD, and the successful surgical treatment of GERD. We review the literature on this relationship between MD and GERD, and discuss the clinical features of this association. Furthermore, the possible cause of the onset of GERD complicated with MD is explored in this report.