Background: Pulmonary arterial hypertension (PAH) is a life-threatening disease with different etiologies and outcomes. We aimed to explore differences in clinical features and outcomes of idiopathic PAH (iPAH) and connective tissue disease-related PAH (CTD-PAH) in Taiwanese patients and determine risk factors for mortality. Methods: We retrospectively reviewed the medical records of patients with right-sided heart catheterization-diagnosed PAH between January 2005 and December 2015. The iPAH (n = 31) and CTD-PAH (n = 14) patients were enrolled and followed until December 31, 2019. Between-group comparisons were conducted. Potential predictors of the mortality of PAH were determined using the Cox proportional hazard regression model. Results: CTD-PAH patients had higher levels of N-terminal pro-brain natriuretic peptide (NT-proBNP) and lower predicted diffusing capacity of carbon monoxide (DLCO) than iPAH patients. The mortality rates were similar between CTD-PAH and iPAH (21.4% vs. 22.6%, p = 0.99). A mean pulmonary arterial pressure (mPAP) > 46 mmHg was a predictor of PAH-induced mortality (adjusted hazard ratio 21.8, 95% confidence interval 2.32–204.8). Conclusions: A higher mPAP level, but not underlying CTDs, imposed a significantly increased risk of mortality to patients with PAH.