Background: About 5–10% of adults with congenital heart disease (ACHD) will develop pulmonary arterial hypertension (PAH), which is associated with significant mortality. Studies on risk factors for poor outcome in a contemporary cohort of these patients with PAH associated with CHD (PAH-CHD) are rare. Methods: In this retrospective, single-center study, adult patients with the diagnosis PAH-CHD who had at least one contact as an outpatient or inpatient at the German Heart Centre Munich during the period January 2010–September 2019 were included. Patients with PAH without a CHD were excluded. The primary endpoint was all-cause mortality. Results: Altogether, 158 patients (mean age 39.9 ± 15.4 years, female 64.6%) were included in the study. A pre-tricuspid shunt was present in 17.7%, other shunts in 51.3%, PAH associated with complex CHD in 22.8%, and segmental PAH in 8.2%. An NT-proBNP measurement at baseline was available in 95 patients (60.1%). During a median follow-up of 5.37 years [IQR 1.76–8.63], the primary endpoint occurred in 10 patients (6.7%). On univariate analysis, CRP (log) (HR 3.35, 95% CI (1.07–10.48), p = 0.037), NT-proBNP (log) (HR: 7.10, 95% CI: 1.57–32.23, p = 0.011), and uric acid (HR: 1.37, 95% CI: 1.05–1.79, p = 0.020) were predictors of the primary endpoint. On multivariate analysis, only NT-proBNP (log) (HR: 6.91, 95% CI: 1.36–35.02, p = 0.0196) remained as an independent predictor. Conclusion: NT-proBNP is an independent predictor of all-cause mortality in a contemporary cohort of PAH-CHD patients. The role of CRP and uric acid should be further assessed in future studies.