Background: The Italian government promoted social distancing, in which the suspension of any social event, suspension of all activities practiced in gyms, sports centers and their closure was ordered. The social distancing in the school environment and the use of strategies to limit viral infection are not very compatible with group motor activity and team sports. The aim of this study is to verify the effectiveness of a CrossFit program in order to mitigate the deficits in fitness caused by COVID-19 prevention measures and to evaluate the effects on self-efficacy in a group of young adolescents. Methodsː 30 healthy participants were randomly allocated into an intervention group (IG) that performed the 8 weeks CrossFit training program or control group (CG). Physical fitness tests (i.e., Squat, push-up, lunge, and 20 m run) and psychological measures Regulatory Emotional Self-Efficacy scale (RESE) were performed at baseline and after 8 weeks. Resultsː After 8 weeks, the intervention group showed significant improvements for all fitness tests (p < 0.0001). Additionally, higher scores for the RESE negative and positive (p < 0.0001) scales were found in the intervention group. No statistical differences were found in the control group except for the push up test. Conclusionsː the 8-week CrossFit intervention program could positively affect the general physical well-being and improve the emotional perceived self-efficacy in healthy adolescents.