COVID-19 pandemic due to SARS-CoV-2 has been one of the major global health issues of this aeon. The aim of this study was to evaluate the association of SARS-CoV-2 cycle threshold (Ct) values with multiple factors among COVID-19 patients visiting a tertiary care hospital in Sudurpashchim province of Nepal. A retrospective analysis was performed on the data of randomly selected COVID-19 cases among the total RT-qPCR tested patients from March 2020 to April 2022. The Ct values at the time of patient admission and their clinical outcomes (discharge or death) were compared. Among the COVID-19 patients, survivor group had significantly higher initial Ct value compared to non-survivors [median Ct values 23.21 and 24.39 (P < 0.0001)]. Selected haematological parameters; white blood cells (P<001), neutrophils (P<001), and monocytes (P<0.0001), and all the biochemical parameters were significantly different between these two groups (p < 0.005). Furthermore, significantly increased CRP (61.54±63.00, P<0.0017), D-dimer levels (0.8979± 1.480, P<0.0001), creatinine (0.7931±0.2551, P<0.0001), monocytes (0.6782±0.7981, P<0.0001), and random blood sugar (152.4±34.32, P<0.0001) were observed among non-survivors indicating as cause of disease severity in COVID-19. The findings of this study imply that the Ct value, CRP and D-dimer levels could be a crucial marker for the early detection of severe COVID-19 patients or those at higher risk of developing severe disease. This will eventually help to identify cases requiring immediate and critical medical care and reduce mortality.