Background <p>The time to pharyngeal polymerase chain reaction (PCR) negativity (TPCRN) in patients with coronavirus disease 2019 (COVID-19) is influenced by multiple factors. This study aimed to investigate the association between clinical symptoms of COVID-19 patients and TPCRN.</p> Methods <p>This retrospective study enrolled 486 participants with COVID-19, aged 18–89 years, who were admitted to Shanghai Lingang Makeshift Hospital between April 10, 2022, and May 20, 2022. Clinical data, including patient demographics, clinical symptoms, and TPCRN, were collected and analyzed.</p> Results <p>This study enrolled COVID-19 patients with a median age of 38 years, consisting of 66.05% males and 33.95% females. Stepwise (forward selection) analyses revealed a positive association between TPCRN and the clinical symptoms of throat pain (B = 1.277, 95% CI = 0.592–1.962, <i>P</i> &lt; 0.001) and diarrhea (B = 1.445, 95% CI = 0.382–2.508, <i>P</i> = 0.008) in COVID-19 patients. Logistic regression analysis indicated that throat pain was associated with a lower 7-day negative nucleic acid conversion rate (OR = 0.584, 95% CI:0.362–0.943, <i>P</i> = 0.028), as was diarrhea (OR = 0.435, 95% CI:0.220–0.860, <i>P</i> = 0.017).</p> Conclusion <p>Our findings indicate that throat pain and diarrhea are associated with a longer time to pharyngeal polymerase chain reaction (PCR) negativity. These results may assist in identifying high-risk patients with delayed viral clearance and provide a reference for optimizing clinical management strategies for this patient population.</p> Clinical trial number <p>Not applicable.</p>