(1) Background: Pulmonary embolism (PE) can be fatal. Computed tomography pulmonary angiography (CTPA) can accurately diagnose PE, but it should be used only when reasonable pre-test probability exists. Overtesting with CTPA exposes patients to excess ionizing radiation and contrast media, while PE overdiagnosis leads to the treatment of small emboli unlikely to cause harm. This study assessed trends in CTPA use and diagnostic yield. We also assessed trends in PE hospitalizations and mortality to indicate PE severity. (2) Methods: Analysis of Western Australian linked administrative data for 2003–2015 including hospitalizations, emergency department (ED) attendances, and CTPA performed at hospitals. Age-sex standardized trends were calculated for CTPA use, PE hospitalizations, and mortality (as a proxy for severity). Logistic regression assessed diagnostic yield of CTPA following unplanned ED presentations. (3) Results: CTPA use increased from 3.3 per 10,000 person-years in 2003 (95% CI 3.0–3.6) to 17.1 per 10,000 person-years (16.5–17.7) in 2015. Diagnostic yield of CTPA increased from 12.7% in 2003 to 17.4% in 2005, declining to 12.2% in 2015 (p = 0.049). PE hospitalizations increased from 3.8 per 10,000 (3.5–4.1) in 2003 to 5.2 per 10,000 (4.8–5.5) in 2015. Mortality remained constant at 0.50 per 10,000 (0.39–0.62) in 2003 and 0.42 per 10,000 (0.32–0.51) in 2015. (4) Conclusions: CTPA increased from 2003 to 2015, while diagnostic yield decreased, potentially indicating overtesting. PE mortality remained constant despite increasing hospitalizations, likely indicating a higher proportion of less severe cases. As treatment can be harmful, this could represent overdiagnosis.