The COVID-19 pandemic and the social distancing implemented shortly after influence physical activity levels (PALs). The purpose of this investigation was to evaluate the changes in PAL and factors associated with PALs among Croatian adolescents while considering the impact of community (urban vs. rural living environment). The sample included 823 adolescents (mean age: 16.5 ± 2.1 years) who were tested on baseline (from October 2019 to March 2020; before COVID-19 pandemic in Croatia) and follow-up (in April 2020; during the COVID-19 pandemic and imposed rules of social distancing). Baseline testing included anthropometrics, physical fitness status, and evaluation of PALs, while follow-up included only PALs (evaluated by a standardized questionnaire through an internet application). The results showed a significant influence of the living environment on the decrease of PAL, with a larger decrease in urban adolescents . Logistic regression showed a higher likelihood for normal PALs at baseline in adolescents who had better fitness status, with no strong confounding effect of the urban/rural environment . The fitness status of urban adolescents predicted their PALs at follow-up . The differences between urban and rural adolescents with regard to the established changes in PALs and relationships between the predictors and PALs are explained by the characteristics of the living communities (lack of organized sports in rural areas), and the level of social distancing in the studied period and region/country.