The endoscopic endonasal approach (EEA) provides a direct trajectory to ventral skull base lesions, avoidance of brain retraction, and clear visualization of cranial nerves as they exit skull base foramina. Despite these benefits, the EEA is not without complications. Here, we review published literature highlighting complications associated with the EEA including cerebrospinal fluid (CSF) leak, cranial nerve (CN) dysfunction, pituitary gland dysfunction, internal carotid artery (ICA) injury, infection, and others; we place special emphasis on discussing the prevention of these complications. As widespread adoption of the EEA continues, it becomes critical to educate surgeons regarding potential complications and their prevention while identifying gaps in the current literature to guide future research and advances in clinical care.