Basilar artery (BA) dolichosis is not uncommon in patients with acute isolated pontine infarction. The effect of this abnormal BA geometrical form on the outcomes of pontine infarction has not been closely examined. This study aims to elucidate whether BA dolichosis contributes to a poor 90-day outcome in acute isolated pontine infarction. A total of 101 patients were enrolled with a median age of 65 years. The BA diameter (p = 0.026), basilar artery length (BAL) (p < 0.001), bending length (BL) (p < 0.001) and the proportion of BA bending (p < 0.001) were significantly higher in the BA dolichosis group. A poor outcome was closely associated with the baseline National Institute of Health Stroke Scale (NIHSS) score (p < 0.001), and BL (p = 0.042) as well as the proportions of BA dolichosis (p = 0.007) and BA bending (p = 0.010) in univariate analysis. Multivariate logistic regression analysis determined that BA dolichosis (adjusted OR = 4.724, 95% CI: 1.481~15.071, p = 0.009) and baseline NIHSS score (adjusted OR = 1.805, 95% CI: 1.296~2.513, p < 0.001) were independently associated with a poor outcome at 90 days. In conclusion, BA dolichosis may be a predictor of concern for a poor 90-day outcome in patients with acute isolated pontine infarction.