Sickle cell disease (SCD) is a genetic hematological disorder associated with severe complications, such as vaso-occlusive crises, acute chest syndrome (ACS), and an increased risk of thromboembolic events, including pulmonary embolism (PE). The diagnosis of PE in SCD patients presents challenges due to the overlapping symptoms with other pulmonary conditions. Our previous study revealed that nearly 96% of computed tomography pulmonary angiography (CTPA) scans in SCD patients were negative for PE, highlighting a gap in understanding the significance of CTPA findings when PE is absent. In this retrospective follow-up study conducted at the Salmaniya Medical Complex in Bahrain, we examined SCD patients with HbSS genotypes who underwent CTPA from January 1, 2018, to December 31, 2021, for suspected PE, but the results were negative. The aim of this study was to identify alternative diagnoses and incidental findings from CTPA scans. Experienced radiologists reviewed the CTPA images and reports to assess potential alternative diagnoses and incidental findings, incorporating an additional analysis of chest X-rays to evaluate the diagnostic value of CTPA. Incidental findings were classified based on their location and clinical significance. Among the 230 evaluated SCD patients (average age 39.7 years; 53% male) who were CTPA negative for PE, 142 (61.7%) had identifiable alternative diagnoses, primarily pneumonia (49.1%). Notably, 88.0% of these alternative diagnoses had been previously suggested by chest radiographs. Furthermore, incidental findings were noted in 164 (71.3%) patients, with 11.0% deemed clinically significant, necessitating immediate action, and 87.8% considered potentially significant, requiring further assessment. Notable incidental findings included thoracic abnormalities such as cardiomegaly (12.2%) and an enlarged pulmonary artery (11.3%), as well as upper abdominal pathologies such as hepatomegaly (19.6%), splenomegaly (20.9%), and gallstones (10.4%). This study underscores the limited additional diagnostic yield of CTPA for identifying alternative diagnoses to PE in SCD patients, with the majority of diagnoses, such as pneumonia, already suggested by chest radiographs. The frequent incidental findings, most of which necessitate further evaluation, highlight the need for a cautious and tailored approach to using CTPA in the SCD population.