The objective of this study is to evaluate whether pregnant women receive appropriate treatment, undertreatment, or overtreatment in the emergency department (ED) when they are tested for chlamydia and gonorrhea as compared to non-pregnant women. In a retrospective cohort study, we analyzed visits made to an urban ED from 1 July 2012 to 30 June 2014, with testing for chlamydia and gonorrhea (n = 3908). Using multiple logistic regression, we compared undertreatment and overtreatment in women controlling for pregnancy, age, race, and sexually transmitted infection International Statistical Classifications of Diseases (ICD)-9 coded diagnosis. Pregnant women were significantly more likely to be undertreated when positive for infection as compared to non-pregnant women (OR 2.94; 95% CI, 1.47–5.95) and significantly less likely to be overtreated when negative for infection (OR 0.40; 95% CI, 0.31–0.53) as compared to non-pregnant women. Pregnant women may not be receiving appropriate treatment when they present to the ED with chlamydia or gonorrhea. Attention should be paid to this group when administering chlamydia and gonorrhea treatment to ensure appropriate care and follow-up.