Introduction: Crimean-Congo hemorrhagic fever (CCHF) disease is characterized by symptoms such as fever, headache, muscle aches, and bleeding. In severe cases, it can lead to death. Clinical and biochemical parameters, severity scoring systems, and some new bio- markers are used to predict the course of the disease. The cycle threshold (Ct) value is a measure used to indicate the number of cycles required for the target gene to reach a certain level of fluorescence in the polymerase chain reaction (PCR) test. This study aimed to evaluate the relationship between Ct values detected in PCR tests and disease prognosis. Materials and Methods: This study was conducted between May 2021 and September 2021. Adult patients with positive CCHF PCR test results were included in the study. The presence of CCHF virus-specific RNA in the serum samples of the patients at the time of admission was determined qualitatively by the RT-PCR method. The study aimed to assess the relationship between Ct values and clinical outcomes, including mortality. Results: A total of 168 patients, 62 (36.9%) female, and 106 (63.1%) male, were included in the study. A mortal course was observed in nine patients (5.4%). The Ct threshold value for predicting prognosis in CCHF disease was calculated as 19 using ROC analysis. Among the 39 patients with a Ct value of ≤19, the disease resulted in death in eight (20.5%) cases, while in the group of 129 patients with a Ct value >19, only one (0.8%) patient experienced mortality (p< 0.001). Conclusion: Ct values provide valuable information about the presence and amount of target genes in the sample. In cases where quantitative determination of viral load is not possible, the Ct threshold value is considered a guide for predicting disease prognosis.