Background: Children have a higher chance of decreasing health-related physical fitness during periods of school lockdown due to pandemic situations such as with COVID-19 disease. Aims: To establish the changes in children’s self-perceived physical fitness (SPPF) during pandemic COVID-19 social distancing in a school lockdown and to describe the individual prevalence of changes in SPPF according to sex. Methods: It is an intervention study with a convenient sample, 67 children (6–13 years old; 50.7% girls). An intervention occurred according to the Brazilian Base Nacional Comum Curricular (BNCC) and the State Education Secretary orientations for remote Physical Education classes. SPPF was evaluated through a questionnaire (QAPA). Generalized estimative equations (GEE) and the prevalence of changes in individual score delta (Δ) from baseline to follow-up determined the effects. Results: Positive individual changes in SPPF were observed for 21.2% of girls and 26.4% of boys. Older children presented fewer SPPF total points. There was no interaction between the evaluation period, sex, and age. However, higher baseline SPPF values presented a negative association with the individual SPPF variation (β = − 2.52%; CI 95% − 3.97 to − 1.07; p = 0.001). Conclusion: A remote Physical Education intervention effectively maintained or even increased individual results of children’s SPPF. Thereby, this study suggests that this kind of initiative should be retained for the duration of social distancing and pandemic conditions to help children maintain an active lifestyle and, consequently, achieve health benefits. Improving intervention effectiveness by focusing on girls seems to be a challenge in this matter.