The endoscopic endonasal approach (EEA) to the craniovertebral junction (CVJ) has recently been considered a safer alternative and less invasive approach than the traditional transoral approach because the complications associated with the latter are avoided or minimized. Here, we present two challenging cases of CVJ pathologies. The first case involved os odontoideum associated with anterior displacement of the occipitocervical junction where the EEA was used, followed by C0-C1-C2 fusion using a posterior approach to decompress the CVJ, and was complicated by rhinorrhea and Candida albicans meningitis. The second case involved basilar invagination with syringomyelia previously treated using a posterior approach, where aggravation of neuropathic symptoms required combined treatment with EEA and occipitocervical fusion of C0-C2-C3-C4, with the postoperative course challenged by operative site infection requiring drainage with debridement and antibiotic therapy. The EEA is an alternative approach for accessing the CVJ in well-selected patients. Knowledge of EEA complications is crucial for the optimal care of patients.