Rifampicin-resistant tuberculosis (RR-TB) remains a major public health concern, and is characterized by diagnostic challenges and suboptimal treatment success. To better understand the factors influencing disease burden and outcomes, the present study investigated the clinical, demographic, radiological, and molecular characteristics of patients in a high-burden tertiary hospital in Indonesia. A cross-sectional study involving adult patients diagnosed with RR-TB at Dr. Soetomo General Hospital (Surabaya, Indonesia) was conducted to analyze clinical symptoms, comorbidities, radiographic findings, treatment regimens, and laboratory data, including sputum smear grades and IS6110–IS1081 cycle threshold (CT) values. Among 55 patients with RR-TB (mean age 45.1 years; 60% male), IS6110–IS1081 CT values exhibited significant inverse associations with the Modified Bandim TB Score (p = 0.002) and chest pain (p = 0.003), indicating higher bacterial burden in more symptomatic patients. CT values were also negatively correlated with sputum smear scores (r = -0.342; p = 0.011). Treatment failure was independently associated with anemia (odds ratio [OR] 13.2, p = 0.023) and a long-course regimen (OR 7.3, p = 0.026). A higher bacterial burden, as reflected by lower IS6110–IS1081 CT values, was associated with greater disease severity and chest pain. Anemia and long-course regimens independently predicted treatment failure, highlighting the need for the early detection of patients at high risk and optimized treatment strategies for RR-TB management.