Aims It is unclear whether thyroid hormones are associated with functional outcome after ischemic stroke. We aimed to investigate the impact of thyroid hormones at admission on functional outcome at 3 months after acute ischemic stroke. Methods A total of 480 consecutive patients for ischemic stroke within 48 hours of onset were enrolled in this study. Thyroid hormones including thyroid-stimulating hormone (TSH), free triiodothyronine (FT3), and free thyroxine (FT4) were measured at admission and functional outcomes were assessed at 3 months with the modified Rankin Scale (mRS) ranging from 0 to 6. Poor outcome was defined as mRS≥3. Results FT3 levels at admission were considerably lower in poor outcome patients than those with good outcome at 3 months (3.53±0.70pmol/L vs 4.04±0.68pmol/L, respectively; P＜0.001). Lower levels of FT3 were observed with higher mRS scores. Multivariable logistic regression analysis revealed that FT3 levels were significantly associated with risk of poor outcome at 3 months independent of conventional risk factors such as age, NIHSS score and recanalized therapy. In addition, patients in the bottom quartile of FT3 levels had a 2.56-fold higher risk of developing poor outcome compared with patients in the top quartile (OR=2.56; 95%CI 1.15-5.69, p =0.021). The sensitivity and specificity of FT3 (≤3.69pmol/L) predicting poor outcome were 62.70% and 72.03% respectively. Conclusion Our study suggests that FT3 levels at admission are significantly and independently associated with risk of poor outcome after ischemic stroke and lower FT3 levels can be regarded as a prognostic biomarker for poor outcome at 3 months.