Objective <p>To verify the association between pre-HSCT functional capacity and the variables of pulmonary function, fatigue, and length of hospital stay.</p> Methods <p>This is a cohort study, involving patients admitted to the bone marrow transplantation. The individuals were submitted to an evaluation in the first 24 h of hospitalization. The length of stay variable was checked on the day of hospital discharge. Functional capacity was assessed through the six-minute walk test (6MWT), and the 30-second sit-to-stand test (SST30) was performed to assess the indirect strength of the lower limbs; moreover, the revised Piper Fatigue Scale was used for the evaluation of the pulmonary function.</p> Results <p>The sample consisted of 35 individuals (19 male; 54%). Fourteen patients achieved a 6MWT ≥80% predicted. The mean age of the sample was 45.5 ± 15.2 years, and BMI 27.4 ± 5.4 kg/m². Patients who completed a six-minute walking distance (6MWD) below the predicted value showed significantly lower pulmonary function values for the variables peak expiratory flow (PEF) (%) (<i>p</i> = 0.031), forced expiratory volume in one second (FEV₁) (%) (<i>p</i> = 0.033), and FEV1/forced vital capacity (FVC) (%) (<i>p</i> = 0.027) in relation to the group with better functional capacity. This group showed significantly higher values in the assessment of lower limb fatigue using the Borg scale pre- (<i>p</i> = 0.008) and post- (<i>p</i> = 0.004) 6MWT, longer hospitalization time (<i>p</i> = 0.0014), but with no significant difference in lower limb muscle strength between groups (<i>p</i> = 0.21). A moderate correlation was found between the 6MWD% and FEV1% (<i>p</i> &lt; 0.05).</p> Conclusion <p>Data indicate that starting HSCT treatment with lower-than-expected physical fitness is associated with lower lung function, greater fatigue in the lower limbs, and longer hospital stays.</p>