Objectives This study aimed to identify differences between bipolar disorder patients who experienced cognitive side effects and those who did not experience cognitive side effects due to prescription of mood stabilizers. Methods This study analyzed 350 Korean adults who were diagnosed with bipolar disorder and prescribed mood-stabilizing drugs. The patients were divided into two groups—patients who experienced cognitive side effects and those who did not experience cognitive side effects. We also compared the demographic and clinical characteristics between both groups. Results The number of patients with an untreated illness longer than 1 year was higher in the group of patients who experienced cognitive side effects compared to the group of patients who did not experience cognitive side effects. Further, the number of patients with manic symptoms at onset was higher in the group of patients who experienced cognitive side effects compared to the group of patients who did not experience cognitive side effects. In addition, the proportion of patients in remission was higher in the group of patients who experienced cognitive side effects compared to the group of patients who experienced no cognitive side effects. However, there was no significant difference regarding the type of mood stabilizer used between the groups. On the other hand, more people experienced cognitive side effects as the valproic acid dosage increased. Conclusion Our findings suggest that there are clinical and demographic differences between people who experienced cognitive side effects and those who did not experience cognitive side effects due to prescription of mood stabilizers.