Background: Toothbrushing is a convenient, inexpensive, widespread and culturally accepted method, resulting in an ideal public health outcome. This study aimed to determine the impact of the COVID-19 pandemic on toothbrushing in Peruvian children. Methods: This was a cross-sectional study conducted using a database of children aged 0 to 11 years, with a final sample of 39,124 participants, 15,974 in 2019 (62.03%) and 7088 in 2020 (55.54%). General toothbrushing, daily toothbrushing and minimum frequency of two times a day were dependent variables; the year was considered as the independent variable. In addition, other covariates such as geographical landscape, area of residence, place of residence, altitude, wealth index, health insurance cover, sex and age. Descriptive, bivariate and multivariate statistical analyses were applied. Results: General toothbrushing was 96.19% (n=51 013), daily toothbrushing was 87.47% (n=42 246) and minimum toothbrushing two times a day was 84.53% (n=33 957). In multivariate form, the year presented a negative association with daily toothbrushing (RPa: 0.97; CI95%: 0.96-0.98; p<0.001) and minimum toothbrushing two times a day (RPa: 0.97; CI95%: 0.95-0.98; p<0.001), adjusted for the previously associated co-variables. Conclusions: The year 2020 of the COVID-19 pandemic negatively impacted daily toothbrushing and minimum twice-daily toothbrushing of Peruvian children.