The application of metabolomics for studying modifications in host metabolism due to viral infections has proven to be a game-changing approach. Prior to our study, only one other ‘omics’ study has been carried out that investigates the interplay between the host and CCHFV and its subsequent pathogenesis. We employed NMR spectroscopy, given its advantages in terms of reproducibility, minimal sample preparation, and capability to analyze complex biofluids. Our methodology builds upon the proven success of metabolomics in the research of other viral hemorrhagic fevers such as Ebola, Marburg, and Dengue. Our research underlines the critical role of SAH, a metabolite involved in numerous biochemical reactions. We provide new insights into the metabolic alterations occurring in CCHF patients. These alterations not only shed light on the disease’s pathogenesis but also pave the way for potential biomarkers and therapeutic targets. Among all the metabolites detected, S-Adenosyl-L-homocysteine and Carnosine stood out as the most prevalent, warranting further exploration of their roles in CCHFV pathogenesis and their potential as therapeutic targets.