Background To investigate the impact of low socioeconomic status (SES), indicated by low level of education, occupation and income, on 3 months functional outcome after ischemic stroke. Methods We analyzed data from the China National Stroke Registry (CNSR), a multicenter and prospective registry of consecutive patients with acute cerebrovascular events occurred between September 2007 and August 2008. 11226 patients with ischemic stroke had SES and clinical characteristics data collected at baseline and mRS measured as indicator of functional outcome in 3 months follow up. Multinomial and ordinal logistic regression models were performed to examine associations between SES and the functional outcome. Results At 3 months after stroke, 5.3% of total patients had mRS scored at 5, 11.3% at score 4, 11.1% at score 3, 14.4% at score 2, 34.2% at score 1 and 23.7% at score 0. Compared to patients with educational level of >= 6 years and non-manual laboring, those < 6 years and manual laboring tended to have higher mRS score (P<0.001). Multinomial adjusted odds ratios (ORs) of outcome in manual workers were significantly increased (ORs from 1.38 to 1.87), but OR in patients with less income was not significant. There were similar patterns of association The impact may be stronger in patients aged < 65 years (P = 0.003, P<0.001 respectively) and being male (P = 0.001, P<0.001 respectively). Conclusions Our study provides evidence that people who are relatively more deprived in socioeconomic status suffer poorer outcome after ischemic stroke. The influence of low educational level and manual laboring can be more intensive than low income level on 3-month outcome. Health policy and service should target the deprived populations to reduce the public health burden in the society.