Middle cranial fossa arachnoid cysts (MFACs) are frequently asymptomatic. Here, we report the case of a 10-year-old boy with growth hormone deficiency (GHD) and an MFAC. His linear growth had followed the -2.5 SD line. On physical examination, his height was 120.8 cm (-2.6 SD), and the level of insulin-like growth factor 1 was low (87 ng/mL). GH provocative tests revealed GHD and brain magnetic resonance imaging (MRI) revealed an MFAC. We started treatment with GH replacement therapy (0.175 mg/kg/week). At the age of 12 years and 9 months, there were no interval changes in the features of the MFAC on the brain MRI. As his height was 145.5 cm (-1.7 SD) at the age of 13 years and 4 months, the therapy seems to be successful without sequelae. GH replacement therapy is suggested to be safe and effective to treat patients with GHD associated with arachnoid cysts.