Rationale: Whipple disease is exceptionally rare in patients with lymphoma in China, particularly when presenting with pulmonary symptoms as the initial manifestation. Respiratory involvement is atypical for Whipple disease and may easily be overlooked, especially in patients receiving targeted drug therapy for lymphoma. In such cases, it can be challenging to distinguish between disease progression, drug-induced pneumonia, and infectious etiologies, as the clinical and radiological findings often overlap. Patient concerns: A 39-year-old patient with lymphoma and persistent fever did not respond well to the broad-spectrum antibiotics. Diagnoses: In contrast to traditional pathological examination or tissue periodic acid–Schiff staining, the patient was diagnosed using metagenomic next-generation sequencing of pulmonary alveolar lavage fluid. Interventions: Symptomatic treatment, including anti-infective agents, cough relief, and expectorants, was administered. Bronchoscopy and lung puncture were performed to determine the cause of the disease. Outcomes: Following the confirmation of Tropheryma whipplei by metagenomic next-generation sequencing, targeted antimicrobial therapy was likely initiated. The patient’s symptoms, including the persistent fever, subsequently resolved, indicating a positive response to the appropriate treatment. Lessons: Whipple trophic pneumonia is an opportunistic infection with low incidence. It typically presents with atypical clinical signs and symptoms, making diagnosis challenging based on the imaging findings. It is often misdiagnosed, particularly in patients receiving immunosuppressants. Gene detection in the lung lavage fluid can aid in diagnosis. This case report discusses a patient with lymphoma and Whipple disease, while also reviewing current literature on the bacterium to enhance clinician awareness of its complexities.