This study addresses the challenge of differentiating between bipolar disorder II (BD II) and borderline personality disorder (BPD), which is complicated by overlapping symptoms. To overcome this, a multimodal machine learning approach was employed, incorporating both electroencephalography (EEG) patterns and cognitive abnormalities for enhanced classification. Data were collected from 45 participants, including 20 with BD II and 25 with BPD. Analysis involved utilizing EEG signals and cognitive tests, specifically the Wisconsin Card Sorting Test and Integrated Cognitive Assessment. The k-nearest neighbors (KNN) algorithm achieved a balanced accuracy of 93%, with EEG features proving to be crucial, while cognitive features had a lesser impact. Despite the strengths, such as diverse model usage, it’s important to note limitations, including a small sample size and reliance on DSM diagnoses. The study suggests that future research should explore multimodal data integration and employ advanced techniques to improve classification accuracy and gain a better understanding of the neurobiological distinctions between BD II and BPD.