<p>B-type natriuretic peptide (BNP) is recognized as a useful prognostic biomarker not only in patients with heart failure (HF) but also in those with stroke. However, the relationship between BNP levels in the post-acute stroke phase and walking independence, an important outcome for patients with stroke, remains unclear. This study investigated the association between BNP levels and walking independence in patients during the post-acute stroke phase. This retrospective study included 650 consecutive patients with stroke (median age: 77 years; male: 53.2%) in the post-acute phase. BNP or N-terminal prohormone of BNP (NT-proBNP) levels were measured at admission to the post-acute rehabilitation ward. To investigate the association between BNP levels and walking independence, the patients were divided into two groups: high BNP (BNP ≥ 200 pg/ml or NT-proBNP ≥ 900 pg/ml) and low BNP. Of 650 patients, 329 (50.6%) achieved walking independence during hospitalization. After adjusting for confounding factors, higher BNP levels were significantly associated with lower walking independence (hazard ratio [HR]: 0.54; 95% confidence interval [CI]: 0.36–0.82; <i>p</i> = 0.004). This association remained consistent across subgroups. The group without an HF diagnosis but with high BNP levels was also associated with reduced walking independence compared to the group without an HF diagnosis but with low BNP levels (HR: 0.42; 95% CI 0.25–0.70; <i>p</i> &lt; 0.001). Elevated BNP levels were associated with lower walking independence in patients with stroke during the post-acute phase. BNP levels in the post-acute phase may be a useful marker for risk stratification in stroke recovery.</p>