Aiming to slow down the spread of the COVID-19, a lockdown was declared in the first term of 2020 in many European countries, applying different restrictions measures. Although the psychological effects of home confinement in children have been described, there is a lack of longitudinal research examining the impact of the confinement over time. The present study analyzes the evolution of the psychological wellbeing of children and adolescents from three European countries with different restrictions. Parents of 624 Italian, Spanish, and Portuguese children and adolescents aged 3 to 18 years old completed the “Impact Scale of COVID-19 and Home Confinement on Children and Adolescents” two, five, and eight weeks after the lockdown. Results show a different pattern for each country. Children from Italy, the first European country that applied a lockdown, were better adapted than Spanish and Portuguese children the first two weeks after confinement but they were more psychologically impacted by home confinement at the eight-week assessment. Portuguese children, who followed a general duty of home confinement, were the best adapted to the situation, with no significant differences over time. A significant change was found in anxiety symptoms in Spanish children, with a decrease at the last assessment. Findings suggest that long confinements and hard restrictions affect children, so prevention measures should be applied during confinements to prevent psychological problems in children.