Abstract Objective This study aimed to explore the factor structure of the Beck Depression Inventory, Second Edition (BDI-II) in persons with epilepsy (PWE) and assess its correspondence with validated BDI-II cognitive and somatic-affective factors associated with depression in other populations. Method Retrospective data from 69 PWE (ages 18–72) who completed the BDI-II at a National Association of Epilepsy Centers level 4 epilepsy center were analyzed. Patients with diagnoses of bipolar disorder and schizophrenia spectrum disorders were excluded. An Exploratory Factor Analysis (EFA) using the psych package in R Studio was conducted, allowing factors to correlate with oblique factor rotation. The number of factors was determined using eigenvalues >1 and scree plots. Results Statistical support is strongest for a one-factor solution with eigenvalue 7.91; however, a two-factor solution (Factor two eigenvalue = 1.16) also met criteria. These factors accounted for 30% and 10% of the variance, respectively. Due to the low eigenvalue, few item loadings (3), and low variance explained by the second factor, item-level considerations were implemented to determine whether a two-factor solution added clinically relevant information. Conclusion Although a one-factor solution was best supported by the data, a second factor including sadness, feeling of punishment, and suicidal thoughts may be clinically relevant given elevated suicide risk and qualitative research reporting punishment feelings among PWE.