We developed a novel imaging technique, designated as vortex flow (VF) mapping, which presents a vortex flow visually on conventional two-dimensional (2D) cine MRI. Using it, we assessed circumferential VF patterns and influences on RA thrombus and supraventricular tachycardia (SVT) in AP connection-type Fontan circulation. Retrospectively, we enrolled 27 consecutive patients (25.1 ± 9.2 years) and 7 age-matched controls who underwent cardiac MRI. Conventional cine images acquired using a 1.5-Tesla scanner were scanned for axial and coronal cross section of the RA. We developed “vortex flow mapping” to demonstrate the ratio of the circumferential voxel movement at each phase to the total movement throughout a cardiac cycle towards the RA center. The maximum ratio was used as a magnitude of vortex flow (MVF%) in RA cine imaging. We also measured percentages of strong and weak VF areas (VFA%). Furthermore, in 10 out of 27, we compared VF between previous CMR (3.8 ± 1.5 years ago) and latest CMR. Of the patients, 15 had cardiovascular complications (Group A); 12 did not (Group B). A transaxial image showed that strong VFA% in Group A was significantly smaller than that in Group B or controls. A coronal view revealed that strong VFA% was also smaller, and weak VFA% was larger in Group A than in Group B or controls (P < 0.05, and P < 0.05). Maximum MVF% in Group A was significantly smaller than in other groups (P < 0.001). Univariate logistic analyses revealed weak VFA% on a coronal image, and serum total bilirubin level as factors affecting cardiovascular complications (Odds ratio 1.14 and 66.1, 95% CI 1.004–1.30 and 1.59–2755.6, P values < 0.05 and < 0.05, respectively). Compared to the previous CMR, smaller maximum VMF%, smaller strong VFA%, and larger weak VFA% were identified in the latest CMR. Circumferentially weak VFA% on a coronal image can be one surrogate marker of SVT and thrombus in AP connection-type Fontan circulation. This simple VF assessment is clinically useful to detect blood stagnation.