Background: Quarantine was one of the strategies adopted by governments against the spread of COVID-19. This restriction has caused an increase in sedentary behaviors and a decrease in the practice of physical activity (PA), with a consequent negative impact on lifestyle both in healthy people and in those who need constant practice of PA to combat diseases, such as patients suffering from neuromuscular diseases (NMDs). Hence, this study aimed to compare PA levels among patients with NMD during and after quarantine. Methods: An adapted version of the International Physical Activity Questionnaire Short-Form and the Short-Form Health Survey were administered during COVID-19 quarantine (T0) and after 3 years (T1) to 91 Italian patients with NMDs. Results: We found a significant increase in the total PA level at T1, with no significant changes in vigorous-intensity PA. Moreover, a significant decrease in the PA level was found among the patients with different NMDs. No significant changes in physical component scores and mental component scores were detected. Conclusions: Our results suggest that it would be necessary to provide alternative indoor exercise settings to prevent the adoption of sedentary behaviors.