Background Innate immunity plays an important role in brain ischemic injury, but there are only few studies on the effects of toll-like receptors (TLRs) on cerebral infarction patients up to now. We aimed to evaluate the TLR mRNA expression of patients with different outcomes. Methods Eighty-six cases suffering from cerebral infarction within 14 days were assigned into the good outcome group (n = 47) and the bad outcome group (n = 39) depending on the modified Rankin Scale scores (mRS ≤2 at 90 days following stroke onset was good outcome). We measured the mRNA expression of TLRs in peripheral blood mononuclear cells of patients at 24 hours, 3 days, 4 days, 7 days, and 14 days from onset. The National Institutes of Health Stroke Scale score and infarction volume were assessed on admission and at 7-14 days, respectively. Results Only TLR3 mRNA expression of the good outcome group was higher than that of the bad outcome group at acute and subacute phases. TLR7 expressions of the good outcome group increased within 3 days following stroke onset. Moreover, the two groups had no significant differences in terms of mRNA expressions of TLR2, TLR4, TLR8, and TLR9. The expression of interferon β of the good outcome group was higher than that of the bad outcome group, and it had a positive correlation with the expressions of TLR3 and interferon regulatory factor 3. Conclusions TLR3 and interferon β mRNA expressions were increased in the peripheral blood of ischemic stroke patients with good outcome, which may imply their neuroprotection.