Purpose: To describe the clinical features of a Caucasian female patient with a history of treated gastrointestinal Whipple's disease (WD) who developed new-onset diplopia, with a description of the histopathological features of the extraocular muscle biopsies. Methods: A previously fit 38-year-old Caucasian female presented with acute-onset diplopia after being on a sustained medication regime for biopsy-proven gastrointestinal WD. A magnetic resonance imaging scan of her orbits with gadolinium revealed diffuse enhancement of the bellies of the extraocular muscles bilaterally, particularly the medial rectus, superior rectus, and superior oblique muscles, consistent with an infiltrative myositis. She underwent unilateral extraocular muscle biopsies. Results: The extraocular muscle biopsies contained macrophages between the muscle fibres. These contained periodic acid-Schiff-positive cytoplasmic granules. Immunohistochemistry with an antibody raised to Tropheryma whipplei showed positive staining of the same macrophages. Transmission electron microscopy confirmed the presence of effete T. whipplei cell membranes in lysosomes. Conclusion: This case describes bilateral WD-associated extraocular muscle myositis. The exact mechanism for this unusual presentation is unclear, but both a WD-associated immune reconstitution inflammatory syndrome and treatment failure are possibilities, with a good response observed to antibiotic therapy and adjunctive corticosteroids.