There are limited data on the rate of clot resolution after acute pulmonary embolism and risk factors for residual emboli. The aim of the present study was to investigate the rate of clot resolution over time and identify risk factors of residual emboli in pulmonary embolism patients. We retrospectively analyzed pulmonary embolism patients with follow-up computed tomography (CT) scans taken between day 3 and day 90. The patients were classified into three cohorts, depending on the time of CT scan: day 3-7, day 8-21, and day 22-90. Each cohort was regrouped into the residual embolus and complete resolution groups. The rate of complete resolution of pulmonary emboli was 24% at 3-7 days, 47% at 8-21 days, and 78% at 22-90 days. In a multivariate analysis, independent predictors in each cohort were lobar or larger pulmonary artery pulmonary embolism and a right ventricle/left ventricle diameter ratio within 1 week, lobar or larger pulmonary artery pulmonary embolism at 1-3 weeks, and central pulmonary embolism at 3 weeks to 3 months. The rate of venous thromboembolism (VTE) recurrence, frequency of an adverse outcome, and in-hospital mortality did not differ between the two groups in each cohort. Complete resolution of pulmonary emboli occurred in most pulmonary embolism patients. Regardless of the time interval, larger pulmonary artery involvement by pulmonary emboli was only independent predictor of residual emboli. The presence of residual emboli was not associated with an adverse outcome of pulmonary embolism and rate of VTE recurrence.