Cytomegalovirus (CMV) colitis, ulcerative colitis (UC), and human immunodeficiency virus (HIV) infection represent distinct and complex conditions that pose significant diagnostic and therapeutic challenges, particularly when they occur concurrently. This case highlights a 44-year-old male with a history of UC and newly diagnosed HIV, presenting with refractory gastrointestinal symptoms ultimately attributed to CMV colitis superimposed on UC. Advanced diagnostic modalities, including endoscopic biopsy and polymerase chain reaction (PCR) testing, were instrumental in differentiating CMV colitis from a UC flare, guiding targeted antiviral and immunomodulatory therapies. This report notes the need for routine CMV screening in refractory UC, emphasizing the utility of quantitative PCR in identifying clinically significant infections. The case also highlights the intricate balance required in managing immune dysfunction, infection control, and inflammation in the context of HIV, CMV colitis, and UC. Furthermore, it draws attention to systemic barriers, such as medication access, which can exacerbate disease progression. Through a multidisciplinary approach, this case demonstrates the potential for tailored interventions to achieve favorable clinical outcomes and provides insights for managing similar complex conditions.