The rapid, ongoing and worldwide coronavirus 2019 (COVID-19) pandemic represents a global public health emergency. Our objective was to explore the impact of the COVID-19 pandemic on somatic symptoms among Chinese college and primary school students, to provide reference data pertaining to the mental health of this population in the context of a public health emergency. In February and March 2020, we explored the somatic symptoms and concerns regarding COVID-19 of 399 college and primary school students in Sichuan Province using the Somatic Self-rating Scale (SSS) and a novel questionnaire, respectively. Logistic regression analysis and non-parametric tests were used to analyze the data. The incidence of somatic symptoms among college students was 34.85 (mild, 26.26%; moderate, 8.59%). The incidence of somatic symptoms in primary school students was 2.39% (all mild). Among the entire cohort, concern regarding COVID-19 was positively correlated with the occurrence of somatic symptoms. Somatic symptoms were more likely among college students expressing greater concern regarding the threat to life and health posed by COVID-19, and the efficacy of prevention and control measures. Among primary school students, only the concern for life and health was associated with a higher likelihood of somatic symptoms. Our data indicate that governments and other relevant agencies should implement different measures to prevent and control mental health disorders diseases in primary school and college students.