Magnetic resonance imaging (MRI) can be used to measure cardiac output (CO) non-invasively, which is a paramount parameter in pulmonary hypertension (PH) patients. We retrospectively compared stroke volume (SV) obtained with MRI (SVMRI) in six localisations against SV measured with thermodilution (TD) (SVTD) and against each other in 24 patients evaluated in our PH centre using Bland and Altman (BA) agreement analyses, linear correlation, and intraclass correlation (ICC). None of the six tested localisations for SVMRI reached the predetermined criteria for interchangeability with SVTD, with two standard deviations (2SD) of bias between 24.1 mL/beat and 31.1 mL/beat. The SVMRI methods yielded better agreement when compared against each other than the comparison between SVMRI and SVTD, with the best 2SD of bias being 13.8 mL/beat. The inter-observer and intra-observer ICCs for COMRI were excellent (inter-observer ICC between 0.889 and 0.983 and intra-observer ICC between 0.991 and 0.999). We could not confirm the interchangeability of SVMRI with SVTD based on the predetermined interchangeability criteria. The lack of agreement between MRI and TD might be explained because TD is less precise than previously thought. We evaluated a new method to estimate CO through the pulmonary circulation (COp) in PH patients that may be more precise than the previously tested methods.