Background: Adolescents with borderline personality disorder often have cognitive impairment, but the underlying mechanism for this is not clear. This study was aimed at assessing alterations in regional homogeneity using resting-state functional MRI (fMRI) in adolescents with borderline personality disorder, and evaluating the associations between regional homogeneity and cognitive testing scores. Methods: We enrolled 50 adolescents with borderline personality disorder (age 12–17 years) and 21 age- and sex-matched healthy controls. We performed regional homogeneity and seed-based functional connectivity analysis for both groups. We also performed correlative analysis for regional homogeneity and cognitive testing scores. Results: Compared with healthy controls, adolescents with borderline personality disorder had reduced regional homogeneity values in the frontal cortex (including the left inferior orbitofrontal cortex and the bilateral superior frontal cortex) as well as in the left precuneus in the default mode network. Adolescents with borderline personality disorder also had higher regional homogeneity values in several cortical regions: the right middle temporal gyrus, the right cuneus, the right precentral gyrus and the left middle occipital gyrus. Regional homogeneity values in the left middle occipital gyrus, left inferior orbitofrontal cortex and right superior frontal gyrus were associated with cognitive testing scores in adolescents with borderline personality disorder. We also found increased functional connectivity between the left middle occipital gyrus and right superior frontal gyrus in adolescents with borderline personality disorder. Limitations: This study had a modest sample size, with a possible case selection bias for patients with more severe illness. This cohort also included patients with comorbidities or taking psychotropic medications, which may have confounded study results. Conclusion: Alterations in regional homogeneity and functional connectivity in brain regions that involve the limbic–cortical circuit could be neural correlates for cognitive impairment in adolescents with borderline personality disorder.