Conjunctival squamous cell carcinoma is generally a low-grade malignancy. A 42-year-old man presented with histologic evidence of extra-tumoral perineural invasion associated with an incompletely excised limbal conjunctival squamous cell carcinoma. Despite further surgery, close observation, plaque radiotherapy, and eyelid-sparing orbital exenteration followed by external beam radiotherapy, the patient developed intracranial perineural invasion with involvement of the trigeminal and facial nerves, ultimately resulting in death. Repeated magnetic resonance imaging with contrast failed to detect perineural invasion until late in the course of disease. Awareness of the possibility of perineural invasion in patients with conjunctival squamous cell carcinoma and of its aggressive nature may be life-saving. Nevertheless, even with initial aggressive tumor control, some patients will show an aggressive tumor growth with recurrences.