Background: Wake-up stroke (WUS) accounts for up to 25% of all new ischemic strokes, but debate exists regarding whether WUS differs from non-WUS in previous studies. Our study aimed to investigate the proportion of WUS cases and to examine differences in clinical characteristics and outcomes in these two groups. Methods: Data from acute ischemic stroke patients who presented to the First Affiliated Hospital of Chongqing Medical University between April 2017 and September 2017 were prospectively collected. Admission demographic information, clinical and radiological characteristics, and 3-month functional outcomes were assessed and compared between patients with WUS and those with non-WUS. Poor functional outcome was defined as modified Rankin Scale ≥ 3 at the 90-day follow-up. Risks of poor outcomes for WUS were estimated with logistic regression analysis. Results: A total of 473 eligible patients were included, of which 132 had been diagnosed with WUS (27.9%). Forty WUS patients had poor functional outcomes and 92 WUS patients had good functional outcomes. WUS and non-WUS patients were similar in regard to stroke risk factors, severity, etiology, and prognosis at 90 days (p > 0.05), but WUS patients were more likely to have had previous stroke (p < 0.001) and a tendency of higher albumin levels (p = 0.051). WUS patients show significant differences in terms of age, gender, prior stroke, atrial fibrillation, impaired consciousness at admission, levels of albumin and triglycerides, stroke severity, and stroke etiology between the good outcome group and the poor outcome group (p < 0.05). Multivariate logistic regression analysis showed that age (odds ratio [OR] 1.079, 95% confidence interval [CI] 1.021–1.141; p < 0.05), previous stroke (OR 4.017, 95% CI 1.197–13.484; p < 0.05), and admission National Institutes of Health Stroke Scale (NIHSS) score ≥5 (OR 5.453, 95% CI 1.510–19.696; p < 0.05) were independently associated with an unfavorable outcome of WUS. Conclusions: WUS accounts for 27.9% of 473 ischemic strokes in the Chinese population. WUS and non-WUS patients were similar in terms of stroke risk factors, severity, etiology, and early outcomes. Age, previous stroke, and a high admission NIHSS score were independent risk factors for unfavorable outcomes in patients with WUS.