Clival lesions are diverse and can be classified into primary, originating from notochordal or hematologic derivatives, or secondary tumors arising from the pituitary gland. Clival metastases are rare. The aim of imaging clival lesions is to delineate the disease's epicenter. However, it may not consistently differentiate between diagnoses in locally invasive lesions. We describe a challenging case involving a 51-year-old Chinese female who presented with atypical symptoms of headache and nasal pain. Initial computed tomography and magnetic resonance imaging findings revealed an invasive lesion of the clivus, supporting a diagnosis of either chordoma or chondrosarcoma. A definitive diagnosis was obtained through a transsphenoidal biopsy, which identified the lesion as a pituitary neuroendocrine tumor. The lesion was subsequently completely excised without postoperative complications. This case underscores the necessity of mandatory biopsy for invasive clival lesions, especially those presenting with atypical imaging features, rather than solely relying on imaging for diagnosis. In the era of minimally invasive transnasal endoscopic techniques, these diagnostic approaches routinely achieve a high diagnostic yield and must be considered to guide further treatment and prognosis.