Whipple's disease (WD) is a rare systemic disorder affecting various organ systems, including the gastrointestinal, cardiovascular, and joint systems. This report discusses a case of WD endocarditis likely associated with tocilizumab (TCZ), an immunomodulator used to treat refractory seronegative arthritis, in a patient with coronary artery disease and rheumatoid arthritis. The diagnosis was confirmed through laboratory studies, imaging, and esophagogastroduodenoscopy with biopsies. WD is increasingly recognized as a potential etiology of seronegative arthritis, with joint pain often preceding gastrointestinal symptoms. Immunomodulatory agents such as TCZ, while effective for rheumatoid arthritis, may exacerbate underlying WD, potentially leading to severe complications such as endocarditis. This case reveals the importance of considering WD in patients with refractory arthritis and the necessity of thorough diagnostic evaluation before initiating immunomodulatory therapy. Epidemiological studies indicate a higher prevalence of WD in certain demographics, highlighting the need for targeted screening with noninvasive screening methodologies, such as stool and saliva polymerase chain reaction testing.