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