Severe coronavirus 2019 disease (COVID-19) causes acute hypoxemic respiratory failure requiring invasive mechanical ventilation (IMV). Once these symptoms are resolved, patients can present systemic deterioration. The two objectives of this study were as follows: to describe the results of a pulmonary rehabilitation program (PRP), which is divided into three groups with different numbers of sessions (12, 24, and 36), and to associate the variables of pulmonary function, exercise performance, and functionality with the number of sessions and functional improvement. Prospective, observational study. PRP consisted of aerobic + strength + flexibility exercises under the supervision and individualized into 12, 24, or 36 sessions (12s, 24s, and 36s), depending on the evolution of each patient. At the beginning of the study and immediately after the intervention, forced vital capacity (FVC), maximal inspiratory pressure, 6-minute walk test (6MWT), sit-to-stand test (STS), maximal handgrip strength (HGS), Fatigue Assessment Scale, Post-COVID-19 Functional Status (PCFS), and health-related quality of life (HRQoL) were measured. The proposed PRP demonstrated a positive effect on pulmonary function, exercise performance, and HRQoL, regardless of the number of sessions. A higher score on the PCFS and more days on IMV were associated with the increased likelihood of needing more sessions, whereas more meters on the 6MWT in the initial evaluation was associated with a reduced likelihood of needing more sessions. Finally, more repetitions on the STS and less distance covered on the initial 6MWT were associated with a greater improvement in exercise performance evaluated with the 6MWT. Supervised and individualized PRP for patients with severe post-COVID-19 improves pulmonary function, exercise performance, functionality, and quality of life. Functionality, distance covered on the 6MWT, and the days on IMV are central to the scheduling of the number of sessions for these patients.