Pemphigus is a chronic dermatological disorder caused by an autoimmune response and is associated with a high proportion of comorbidities and fatalities. The aim of this study was to investigate the risk of depression in patients with pemphigus. Data were derived from the National Health Insurance Research Database recorded during the period 2000–2010 in Taiwan. Multivariate Cox proportional hazards regression models were used to analyze the data and assess the effects of pemphigus on the risk of depression after adjusting for demographic characteristics and comorbidities. Patients with pemphigus were 1.98 times more likely to suffer from depression than the control group (pemphigus, adjusted HR: 1.99, 95% CI = 1.37–2.86). People aged ≥65 years were 1.69 times more likely to suffer from depression than those aged 20–49 years (≥65 years, adjusted HR: 1.42, 95% CI = 0.92–2.21). Female and male patients with pemphigus were respectively 2.02 and 1.91 times more likely to suffer from depression than the control group (female, adjusted HR: 2.09, 95% CI = 1.24–3.54; male, adjusted HR: 1.87, 95% CI = 0.97–3.60). People with HTN, hyperlipidemia, asthma/COPD, and chronic liver disease were respectively 1.73, 2.3, 2.2, and 1.69 times more likely to suffer from depression than those without these comorbidities (HTN, adjusted HR: 0.75, 95% CI = 0.41–1.42; hyperlipidemia, adjusted HR: 1.48, 95% CI = 0.78–2.82; asthma/COPD, adjusted HR: 1.4, 95% CI = 0.72–2.69; and chronic liver disease, adjusted HR: 1.61, 95% CI = 1.07–2.43). There was a significant association between pemphigus and increased risk of depression. Female patients had a higher incidence of depression.