Chordoma is a malignant notochordal tumour, arising primarily in the bones of the base of the skull, the vertebral bodies, and the sacrococcygeal bones. It is a very rare, locally aggressive malignant tumour with an incidence of only one in one million population. In this tertiary care institute only eleven cases had been diagnosed over a period of five years, from 2010 to 2015. We present here the cytologic findings of a case of chordoma arising in the suboccipital region of a twenty year old girl, along with its radiologic and histopathologic correlation. The initial radiologic diagnosis was clival chordoma, and subsequent fine needle aspiration cytology and histopathologic examination confirmed the diagnosis. Cytology showed cellular smears with the typical physaliphorous cells of chordoma in an abundant myxoid background. The patient was treated by radiotherapy. The characteristic cytomorphologic features of chordoma allow accurate diagnosis by fine needle aspiration biopsy. In this case, the diagnosis of chordoma was done by radiology followed by cytologic examination, and was confirmed by histopathology.