Although middle fossa arachnoid cysts (MFACs) are common, the optimal surgical treatment for these lesions remains controversial. In this study, we present our experiences of treating MFACs by microsurgical fenestration and evaluate its effectiveness. We performed retrospective review of 28 patients who underwent microsurgical fenestration for MFACs between May 2003 and December 2014. We reviewed patient characteristics and treatment outcomes including age, sex, symptoms, complicating hydrocephalus, Gallasi classification, change in cyst size after surgery, complicating subdural hygroma, symptom resolution, regrowth of the cyst, and reoperation (including additional CSF diversion). Twenty-eight MFACs in 28 patients were investigated. The average age at the time of surgery was 61.6months. The average follow-up duration was 53.5months. After surgery, 19 (90.5%) of 21 patients with symptomatic MFACs experienced improvements. The cysts decreased in size in all cases (100%, 28/28) and disappeared in three cases (11%, 3/28). None of the cases experienced regrowth of the cyst. Subdural hygroma was identified in 23 cases (82.1%) at the immediate postoperative period. Hygroma was asymptomatic in all cases but one. Hygroma disappeared in 19 cases (83%) and decreased in size in three cases (13%) in the long term. Only one case (4%) required an additional subdural-peritoneal shunt. The rate of CSF diversion after the fenestration was significantly higher in patients with preoperative ventricular dilation (p = 0.0002). Microsurgical fenestration for pediatric MFACs was considered to be safe and effective. Although subdural hygroma developed in significant number of patients at the immediate postoperative period, it was mostly asymptomatic and disappeared or decreased in size in the long term.