Introduction: COVID-19 is an emerging pandemic disease caused by severe acute respiratory syndrome (SARS-CoV-2). Although most patients infected with SARS-CoV-2 are asymptomatic or have mild symptoms, some patients develop severe symptoms that can long-term impair their quality of life and functional capacity. SARS-CoV-2 is closely related to severe acute respiratory syndrome (SARS) with direct and indirect effects on several systems, especially the musculoskeletal system, in addition to the respiratory system. Some of these symptoms persist for a long time, called Post-COVID-19 Syndrome, directly interfering with the functional capacity and quality of life of these patients. Pilates exercises focus on breathing, postural symmetry, trunk stabilization, flexibility, joint mobility and strengthening through the full range of motion of all joints and not isolated muscle groups. Objectives: The objective of this study will be to evaluate the clinical and functional effects of a Pilates exercise program for patients with Post-Covid-19 syndrome after a period of intensive care admission and invasive mechanical ventilation. Methods: The study will be a clinical, randomized and controlled trial. 48 patients of both sexes, over 18 years of age, who have developed the severe form of COVID-19 and required at least 7 days of invasive mechanical ventilation will be recruited. Patients who currently require supplemental oxygen at home and who present motor, cognitive or neurological alterations that prevent the practice of Pilates will be excluded. They will be previously randomized in a 1:1 ratio by electronic system and blindly allocated to the intervention group that will perform an exercise protocol based on the Pilates method, 2x/week, for 12 weeks in therapeutic sessions of identical protocols lasting 60 min. All patients will be evaluated before and after for six minutes walk distance test, peripheral and respiratory muscle strength and endurance, post-COVID-19 functional status, dyspnea, fatigue and quality of life. The analysis of the data obtained during the research was carried out by an independent statistician who had access to the coded data and were based on intention-to-treat principles. Missing data will be assumed to be completely missing by chance. Multiple imputation was used to explain these missing data (STERNE et al., 2009). Missing values in the outcome variables were estimated using multiple imputation by chained equations after 50 imputed replicated data sets. Variables included in the multiple imputation process included (1) group factor, (2) time factor, and (3) the respective outcome variable. Descriptive statistics will be used to present the characteristics of participants in the two treatment groups. P values less than 0.05 will be considered to indicate statistical evidence of significance. The variables of fatigue, peripheral muscle strength, functional capacity, post-COVID functional status and HRQoL were analyzed using linear models of repeated measures (participants and time as random factors) which included all values measured after randomization with baseline scores and treatment clusters as covariates. Adjusted mean differences will be tested 12 weeks after randomization and start of intervention. Multiple comparisons were performed using the Tukey Test with p-values adjusted using the Holm procedure. Baseline variables were evaluated as predictors and moderators of treatment effects, including terms and interaction models. Effect sizes for primary and secondary endpoints were calculated as Cohen's d from estimated marginal means (SMD) and standard error estimates from the adjusted primary analysis. Effect sizes were interpreted according to Cohen's criteria (small ≤0.2; moderate=0.5; large ≥0.8)(COHEN, 1988). All analyzes were performed using RStudio version 0.99.486. Results: The expected results are based on the alternative hypothesis that Pilates exercises are clinically effective, improving functional performance, exercise tolerance, reducing symptoms and improving the quality of life of patients with symptoms of Post-COVID-19 Syndrome.