Due to the decreasing trends in daily confirmed COVID-19 cases and daily confirmed tests, there is a need for a new testing system capable of quickly and efficiently testing small amounts of samples. Therefore, we compared and evaluated the testing performance of the Aptima SARS-CoV-2 assay, an automated testing system that allows continuous loading of samples, and the Real-Q Direct SARS-CoV-2 detection kit that is currently being used in our laboratory. We compared the results of the two testing systems using 259 residual individual nasopharyngeal specimens and 91 residual pooled nasopharyngeal specimens that were submitted for COVID-19 testing in January and February 2023. The 95% limit of detection (LoD) for the Aptima SARS-CoV-2 assay determined using reference material for SARS-CoV-2 nucleic acid was confirmed to be 17.793 copies/mL, while the LoD for the Real-Q Direct SARS-CoV-2 detection kit was determined to be 131.842 copies/mL for the RdRP gene and 241.77 copies/mL for the E gene. The comparative study using clinical specimens showed almost perfect agreement. Our data showed that the Aptima SARS-CoV-2 assay has a very low LoD. In addition, the Aptima SARS-CoV-2 assay and Real-Q Direct detection kit have comparable clinical performance for SARS-CoV-2 for individual and pooled samples.