In patients with heart failure (HF), the impact of the Geriatric Nutritional Risk Index (GNRI) on in-hospital mortality and length of hospital stay remains unclear. We aimed to identify the factors associated with increased in-hospital mortality and longer length of hospital stay considering the GNRI in acute decompensated HF with reduced and preserved ejection fraction (HFrEF and HFpEF, respectively). Patients with acute decompensated HF who were admitted to our institution between 2007 and 2011 were investigated. A total of 451 (201, HFrEF; 250, HFpEF) patients were divided into the following: patients with GNRI < 92 and ≥92. In HFrEF, there were no significant differences in in-hospital mortality and length of hospital stay between patients with GNRI < 92 and ≥92 (median (interquartile range), 24.0 (23.8) days and 20.0 (15.0) days, respectively, p = 0.32). In HFpEF, despite no differences in in-hospital mortality, patients with GNRI < 92 had significantly longer length of hospital stay than those with GNRI ≥ 92 (median (interquartile range), 20.0 (22.3) days and 17.0 (16.0) days, respectively, p = 0.04). In HFpEF, GNRI < 92, along with lower hemoglobin, higher B-type natriuretic peptide, and elevated C-reactive protein levels, were the independent factors for longer length of hospital stay. Among patients with acute decompensated HF, assessment of nutritional status with GNRI is useful for stratifying patients at high risk for longer length of hospital stay in HFpEF but not in HFrEF. These observations are particularly important when considering the increasing elderly population and prevalence of HFpEF.