Background Previous research has demonstrated an association between anaemia and poor outcomes in acute stroke. This study aimed to assess the impact of anaemia on stroke by anaemia subtype. Methods Data from a prospective UK Regional Stroke Register were used to assess the association between hypochromic microcytic and normochromic normocytic anaemia on inpatient-mortality, length of stay (LOS) and discharge modified Rankin scale (mRS). Analysis was stratified by stroke subtypes and multivariable logistic regression, adjusting for potential confounders, was used to quantify this association. Patients who were not anaemic were the reference category. Results A total of 8167 stroke patients (admitted between 2003 and 2015) were included, mean age (SD) 77.39 ± 11.90 years. Of these, 3.4% (n = 281) had hypochromic microcytic anaemia and 15.5% (n = 1262) had normochromic normocytic anaemia on admission. Normochromic normocytic anaemia was associated with increased odds of in-patient mortality OR 1.48 (1.24–1.77), 90-day mortality OR 1.63 (1.38–1.92), longer LOS OR 1.21 (1.06–1.40), defined as > 7 days, and severe disability defined as discharge mRS ≥ 3 OR 1.31 (1.06–1.63), in patients with ischaemic stroke. Hypochromic microcytic anaemia was associated with 90-day mortality OR 1.90 (1.40–2.58) and a longer LOS OR 1.57 (1.20–2.05) in patients with ischaemic stroke. Conclusions Hypochromic microcytic and normochromic normocytic anaemia are associated with differing outcomes in terms of inpatient mortality and post stroke disability. While it is unclear if anaemia per se or another underlying cause is responsible for adverse outcomes, subtype of anaemia appears to be relevant in stroke prognosis.