Prediction of post-stroke functional outcome is important for personalized rehabilitation treatment, we aimed to develop an effective nomogram for predicting long-term unfavorable functional outcomes in ischemic stroke patients after acute phase. We retrospectively analyzed clinical data, rehabilitation data, and longitudinal follow-up data from ischemic stroke patients who underwent early rehabilitation at multiple centers in China. An unfavorable functional outcome was defined as a modified Rankin Scale (mRS) score of 3-6 at 90 days after onset. Patients were randomly allocated to either a training or test cohort in a ratio of 4:1. Univariate and multivariate logistic regression analyses were used to identify the predictors for the development of a predictive nomogram. The area under the receiver operating characteristic curve (AUC) was used to evaluate predictive ability in both the training and test cohorts. A total of 856 patients (training cohort: = 684; test cohort: = 172) were included in this study. Among them, 518 patients experienced unfavorable outcomes 90 days after ischemic stroke. Trial of ORG 10172 in Acute Stroke Treatment classification ( = 0.024), antihypertensive agents use odds ratio (OR) = 1.86; = 0.041, 15-day Barthel Index score (OR = 0.930; < 0.001) and 15-day mRS score (OR = 13.494; < 0.001) were selected as predictors for the unfavorable outcome nomogram. The nomogram model showed good predictive performance in both the training (AUC = 0.950) and test cohorts (AUC = 0.942). The constructed nomogram model could be a practical tool for predicting unfavorable functional outcomes in ischemic stroke patients underwent early rehabilitation after acute phase.