Objective To investigate the predictive factors of progressive motor deficits (PMD) after isolated pontine infarction. Methods Consecutive patients with isolated pontine infarction admitted to hospital within 48 hours after onset were enroled. They were divided into either a PMD group (increase ≥1 within 7 days) or a non-PMD group according to the clinical course and the changes of motor scores of the National Institutes of Health Stroke Scale (NIHSS). The pontine infarction patterns were classified as basal surface infarction and deep infarction, the sides were divided into left and right, the infarct levels were divided into upper, middle, and lower according to diffusion-weighted imaging. The demographics, baseline clinical data, and imaging features were compared between the two groups. Multivariable logistic regression models were used to analyze the predictive factors of PMD after isolated pontine infarction. Results A total of 101 patients with isolated pontine infarction admitted to hospital within 48 h of onset were enroled, including 16 in the PMD group and 85 in the non-PMD group. The proportions of pontine infarction involving the basal surface (87. 5% vs. 47. 1% , χ2 = 8. 851, P = 0. 003), the infarcts on the middle levels (56. 2% vs. 24. 7% , χ2 = 4. 851, P = 0. 028), and basilar artery stenosis or occlusion (62. 5% vs. 27. 1% ,χ2 = 7. 689, P = 0. 006) of the PMD group were significantly higher than those of the non-PMD group, while the proportions of the infarcts on the left sides (18. 8% vs. 56. 5% , χ2 = 7. 664, P = 0. 006) and the infarcts on the upper levels (37. 5% vs. 72. 9% , χ2 = 7. 689, P = 0. 006) of the PMD group was significantly lower than those of the non-PMD group. Multivariate logistic regression analysis identified that pontine infarction involving the basal surface (odds ratio 5. 650, 95% confidence interval 1. 011 - 31. 580, P = 0. 049) and basilar artery stenosis or occlusion (odds ratio 4. 075, 95% confidence interval 1. 127 - 14. 741, P = 0. 032) were the independent risk factors for PMD after isolated pontine infarction. Conclusions Infarction involving the basal surface and basilar artery stenosis or occlusion may be the predictors for PMD after isolated pontine infarction.