Background and Objectives: Coinfection with SARS-CoV-2 and extrapulmonary tuberculosis (extraPTB) presents unique clinical challenges due to dual inflammatory responses and potential differences in patient profiles compared to those with SARS-CoV-2 infection alone. This study uniquely contributes to the underexplored interaction between extraPTB and SARS-CoV-2, focusing on systemic inflammation as a critical determinant of outcomes. Materials and Methods: This retrospective, cross-sectional study included 123 patients aged 19–91 years, hospitalized at Victor Babeș Hospital in Timișoara from March 2020 to March 2022. We compared 23 extraPTB and SARS-CoV-2 coinfected patients with 100 age-matched SARS-CoV-2-only patients. Clinical records were examined for demographic, clinical, and laboratory data. Results: The coinfected group was younger, with 65% under 40 years, and presented significantly higher IL-6, PCT, and transaminase levels. Coexisting COPD and type 2 diabetes were independent predictors of coinfection. A higher SpO2 at diagnosis was positively associated with coinfection likelihood (OR = 5.37), while CT scores indicated less pulmonary involvement in coinfected patients. Non-fatal outcomes were more frequent in the coinfection group (95.7% sensitivity), and only one coinfected patient had a fatal outcome versus 17 in the SARS-CoV-2-only group. Low SpO2 and elevated IL-6 were significant predictors of mortality, with severe symptoms tripling fatality odds. Conclusions: Coinfection with extraPTB and SARS-CoV-2 is associated with younger age, heightened systemic inflammation, and longer hospital stays but does not significantly increase mortality risk compared to SARS-CoV-2 alone. These findings underscore the importance of monitoring systemic inflammatory markers and developing tailored management strategies to improve long-term care outcomes for coinfected patients, especially in resource-limited settings.