We aimed to evaluate the clinical utility of stationary tissue background phase correction for affecting precision in the measurement of Qp/Qs by cardiovascular magnetic resonance (CMR). We enrolled consecutive patients (n = 91) referred for CMR at 1.5T without suspicion of cardiac shunt, and patients (n = 10) with verified cardiac shunts in this retrospective study. All patients underwent phase contrast flow quantification in the ascending aorta and pulmonary trunk. Flow was quantified using two semi-automatic software platforms (SyngoVia VA30, Vendor 1; Segment 2.0R4534, Vendor 2). Measurements were performed both uncorrected and corrected for linear (Vendor 1 and Vendor 2) or quadratic (Vendor 2) background phase. The proportion of patients outside the normal range of Qp/Qs was compared using the McNemar's test. Compared to uncorrected measurements, there were fewer patients with a Qp/Qs outside the normal range following linear correction using Vendor 1 (10% vs 18%, p < 0.001), and Vendor 2 (10% vs 18%, p < 0.001), and following quadratic correction using Vendor 2 (7% vs 18%, p < 0.001). No patient with known shunt was reclassified as normal following stationary background correction. Therefore, we conclude that stationary tissue background correction reduces the number of patients with a Qp/Qs ratio outside the normal range in a consecutive clinical population, while simultaneously not reclassifying any patient with known cardiac shunts as having a normal Qp/Qs. Stationary tissue background correction may be used in clinical patients to increase diagnostic precision.