The incidence of unplanned reoperation after surgery during the same hospitalization is considered one of most important evaluation indicators for health care quality. The purpose of this study was to determine the incidence and risk factors related to unplanned reoperation after an endoscopic endonasal approach (EEA). All patients who underwent elective endoscopic endonasal surgery from January 2016 to December 2021 in the Department of Neurosurgery, Tangdu Hospital, Air Force Military Medical University, were included. We identified the patients who underwent an unplanned reoperation and those who did not and divided them into two groups. The demographic data and risk factors were compared between the groups by univariate and multivariate logistic regression analyses. Of the 1783 patients undergoing EEA for various lesions of the skull base, the incidence of unplanned reoperation was 2.3%. The most common unplanned reoperations were repair of cerebrospinal fluid (CSF) leakage (39%), sellar hematoma evacuation (34.1%), hemostasis of epistaxis (14.6%) and external ventricular drainage for obstructive hydrocephalus (9.8%). The maximum diameter of tumor ≥ 3 cm (OR 2.654, CI 1.236-5.698; p = 0.012), meningioma (OR 4.198, CI 1.169-15.072; p = 0.028), craniopharyngioma (OR 5.020, CI 2.020-12.476; p = 0.001) and other sellar lesions (OR 4.336, CI 1.390-13.527; p = 0.012) and an operation time ≥ 240 min (OR 2.299, CI 1.170-4.518; p = 0.016) were the independent risk factors for unplanned reoperations in multivariate regression analysis. Of the 41 patients undergoing unplanned reoperation, 16 patients died, twenty-one patients had panhypopituitarism, 13 patients had transient and 6 had permanent diabetes insipidus, and 11 patients presented with intracranial infection and 6 of these patients were cured. By reviewing our department's data, we stated the incidence and risk factors for unplanned reoperation. It is important for the hospital administration and neurosurgeons to place more emphasis on these indicators. Furthermore, we suggest some effective quality improvement initiatives to reduce the incidence of unplanned reoperation.