Abstract Objectives: This study aimed to identify the related risk factors and potential predictors of SARS-CoV-2 RNA negative conversion by describing the dynamics of viral shedding in infected children admitted to two hospitals from Shanghai during Omicron variant outbreak. Methods: This retrospective cohort included laboratory-confirmed cases of SARS-CoV-2 infection from Shanghai between March 28 and May 31, 2022. Clinical characteristics, personal vaccination, household vaccination rates were collected through electronic health records and telephone interviews. Results: The total of 603 pediatric cases confirmed with COVID-19 was included in this study. Both Univariate and multivariate analysis were performed to filter independent factors for the duration to viral RNA negative conversion. Data on cases re-detected SARS-CoV-2 after showing negative results on RT-PCR test (intermittent negative status) were also analyzed. The median duration of virus shedding was 12(Interquartile Qange,IQR: 10-14) days. The severity of clinical outcome, personal vaccination-2doses, household vaccination rates, abnormal defecation were factors indecently affecting negative conversion of SARS-CoV-2 RNA, suggesting that patient who had abnormal defecation or with more severe condition would delay virological clearance, while patient accepted 2 doses vaccination or with higher household vaccination rates would accelerate virological clearance. Loss of appetite (Odds Ratio (OR) :5.343; 95%CI: 3.307-8.632) and abnormal defecation (OR:2.840; 95%CI: 1.736-4.645) were significantly associated with intermittent negative status. Conclusion: These findings could provide clues for early identification of pediatric patients with prolonged viral shedding, enriching the evidence for development of prevention and control strategies especially the vaccination policies for children and adolescents.