Objective It was aimed to reveal the continuing perfusion defect rates in patients with a diagnosis of pulmonary embolism (PE) due to COVID-19 who have completed the third month of anticoagulant therapy but whose symptoms or laboratory elevations continue. Methods Patients with COVID-19 who were diagnosed with PE by Q-SPECT-CT between 1 September 2020 and 1 November 2021, who underwent control Q-SPECT/CT were included in the study. Demographic characteristics, laboratory findings, and first and second Q-SPECT/CT evaluation results of the patients were recorded. Results It was observed that the pulmonary defect continued in Q-SPECT/CT in the third month of anticoagulant treatment in 58.3% of the patients diagnosed with PE due to COVID-19, and new defects developed in 6.3%. The persistence rate of segment defects was higher than that of subsegment defects. It was observed that the defects persisted more frequently in patients with a history of hospitalization due to COVID-19. Conclusion Perfusion defects may still be present in patients diagnosed with PE due to COVID-19 in the presence of persistent dyspnea/chest pain/D-dimer elevation after 3 months of treatment. Perfusion defect persistence rates are higher in defects more proximal to the subsegment level and in people with severe COVID-19, and extended treatment should be considered in these patients.