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Background and aims The COVID-19 pandemic significantly impacted high-performance athletes (HPAs) by affecting their training and participation in competitions due to cancellations. The aim of this study is to analyze HPAs’ physical activity, sedentary behavior, and mental health during and after the COVID-19 lockdown while considering sex and type of sport. Materials and methods A repeated-measures observational study with a census sampling approach (N = 556) HPAs from a public university in Mexico. Informed consent was obtained, and a survey was administered in person and online. Physical activity and sedentary behavior were measured using the International Physical Activity Questionnaire (IPAQ), and mental health was assessed using the Profile of Mood States (POMS). Percentages, means, standard deviations, Student’s t-test, and Kruskal–Wallis tests were analyzed. Results Participants were an average age of 19.5 years; 50.2% were male, 55.9% practiced ball sports, 28.5% engaged in athletic sports, and 15.6% participated in combat sports. During confinement, 63.1% reported a high level of physical activity, which increased to 89.4% after confinement (X2 = 20.37, p < 0.0001). Moreover, 86% exhibited sedentary behavior during confinement, which decreased to 57.9% afterward (p < 0.00001). No significant differences were found considering sex or type of sport. Regarding mental health, significant improvements were observed in all dimensions by sex and type of sport (p < 0.05), except for the vigor dimension. Conclusions The lockdown impacted HPAs’ physical activity levels and mental health. After confinement, athletes increased their levels of vigorous physical activity and reduced sedentary behavior, reflecting adaptation to the new circumstances. Mental health indicators improved post-lockdown, although differences by sex and type of sport persisted in certain aspects.