A significant increase in the use of computed tomography with pulmonary angiography (CTPA) for the diagnosis of pulmonary embolism (PE) has been observed in the past twenty years. We aimed to investigate whether the validated diagnostic predictive tools and D-dimers were adequately utilized in a large public hospital in New York City. We conducted a retrospective review of patients who underwent CTPA for the specific indication of ruling out PE over a period of one year. Two independent reviewers, blinded to each other and to the CTPA and D-dimer results, estimated the clinical probability (CP) of PE using Well’s score, the YEARS algorithm, and the revised Geneva score. Patients were classified based on the presence or absence of PE in the CTPA. A total of 917 patients were included in the analysis (median age: 57 years, female: 59%). The clinical probability of PE was considered low by both independent reviewers in 563 (61.4%), 487 (55%), and 184 (20.1%) patients based on Well’s score, the YEARS algorithm, and the revised Geneva score, respectively. D-dimer testing was conducted in less than half of the patients who were deemed to have low CP for PE by both independent reviewers. Using a D-dimer cut-off of <500 ng/mL or the age-adjusted cut-off in patients with a low CP of PE would have missed only a small number of mainly subsegmental PE. All three tools, when combined with D-dimer < 500 ng/mL or <age-adjusted cut-off, yielded a NPV of > 95%. All three validated diagnostic predictive tools were found to have significant diagnostic value in ruling out PE when combined with a D-dimer cut-off of <500 ng/mL or the age-adjusted cut-off. Excessive use of CTPA was likely secondary to suboptimal use of diagnostic predictive tools.