Anxiety and depression commonly co-occur during pregnancy and may increase risk of poor birth outcomes including preterm birth and low birth weight. Our understanding of rates, patterns, and predictors of comorbid anxiety and depression is hindered given the dearth of literature, particularly in low- and middle-income (LMI) countries. The aim of this study is (1) to explore the prevalence and patterns of comorbid antenatal anxiety and depressive symptoms in the mild-to-severe and moderate-to-severe categories among women in a LMI country like Pakistan and (2) to understand the risk factors for comorbid anxiety and depressive symptoms. Using a prospective cohort design, a diverse sample of 300 pregnant women from four centers of Aga Khan Hospital for Women and Children in Pakistan were enrolled in the study. Comorbid anxiety and depression during pregnancy were high and numerous factors predicted increased likelihood of comorbidity, including: (1) High level of perceived stress at any time point, (2) having 3 or more previous children, and (3) having one or more adverse childhood experiences. These risks were increased if the husband was employed in the private sector. Early identification and treatment of mental health comorbidities may contribute to decreased adverse birth outcomes in LMI countries.