Background: Contrast computed tomography (CT) is a useful tool for the detection of intracardiac thrombi. We aimed to assess the accuracy of the late-phase prone-position contrast CT (late-pCT) for thrombus detection in patients with persistent or long-standing persistent atrial fibrillation (AF). Methods: Early and late-phase pCT were performed in 300 patients with persistent or long-standing AF. If late-pCT did not show an intracardiac contrast defect (CD), catheter ablation (CA) was performed. Immediately prior to CA, intracardiac echocardiography (ICE) from the left atrium was performed to confirm thrombus absence and the estimation of the blood velocity of the left atrial appendage (LAA). For patients with CDs on late-pCT, CA performance was delayed, and late-pCT was performed again after several months following oral anticoagulant alterations or dosage increases. Results: Of the 40 patients who exhibited CDs in the early phase of pCT, six showed persistent CDs on late-pCT. In the remaining 294 patients without CDs on late-pCT, the absence of a thrombus was confirmed by ICE during CA. In all six patients with CD-positivity on late-pCT, the CDs vanished under the same CT conditions after subsequent anticoagulation therapy, and CA was successfully performed. Furthermore, the presence of residual contrast medium in the LAA on late-pCT suggested a decreased blood velocity in the LAA (≤ 15 cm/s) (sensitivity = 0.900 and specificity = 0.621). Conclusions: Late-pCT is a valuable tool for the assessment of intracardiac thrombi and LAA dysfunction in patients with persistent or long-standing persistent AF before CA.