Background More than half of the predicted cervical cancer deaths are expected to be prevented with improved screening and management strategies. However, the conventional cervical screening procedure is considered as uncomfortable and embarrassing for most women in developing countries, such as Indonesia, leading to a low participation rate of screening. In response, we assessed the performance of the newly developed hrHPV ReadyMix qPCR Kit to detect high-risk human papillomavirus (HPV) in urine samples and conduct simultaneous genotyping of HPV16, HPV18, and HPV52. Methods We enrolled women aged 20-50 years from three cities in Indonesia, specifically Jakarta, Bandung, and Semarang. Participants were instructed to provide self-collected first-void urine samples, followed by a physician-assisted cervical swab sample collection. Nucleic acids were then extracted and tested for HPV with Roche cobas 6800 HPV and hrHPV ReadyMix qPCR kit. Next generation-sequencing (NGS) was employed in cases of discrepant results. hrHPV ReadyMix diagnostics accuracy were assessed against Roche cobas 6800 HPV as a reference test and the utility of urine samples as an alternative sampling method were compared to the standard cervical swab samples. Results 876 paired samples were analysed for HPV detection. The sensitivity of HPV detection in cervical swabs using hrHPV ReadyMix qPCR Kit reached 96.55% and the specificity reached 99.87%. Despite having a tendency to produce higher Ct value in high-risk HPV detection, urine samples produced a high sensitivity at 80.88% and a specificity of 100.00% when compared to cervical swabs. Our developed method enables population-based high-risk HPV analysis with 6.62% HPV prevalence based on cervical swabs and 6.28% HPV prevalence based on urine samples. Urine samples, tested with the hrHPV ReadyMix qPCR Kit, exhibited comparable HPV positivity rate to cervical swabs and similar genotyping capability of HPV16 and HPV18 as the Roche cobas 6800 HPV system. Conclusions We demonstrated that self-collected urine samples can be an alternative specimen to detect HPV infection with a diagnostic accuracy of 98.48%. This study highlights the potential of the hrHPV ReadyMix qPCR Kit in improving cervical cancer screening and provides valuable insights for future interventions.