We report the case of a middle-aged man where a diagnosis of pulmonary embolism (PE) was delayed due to initial underestimation of risk and over-reliance on D-dimer testing. The patient presented with pleuritic chest pain after a 5 h domestic flight. The treating clinicians presumed that this duration of immobilisation was insufficient to cause a PE, D-dimer was not measured and the patient was discharged home. One week later, the patient re-presented due to persistence of chest pain. On this occasion, D-dimer was measured and it was normal, which was interpreted as excluding a PE. Subsequently, a CT pulmonary angiogram was performed, which demonstrated a subsegmental PE. This case highlights the importance of accurate assessment of PE-risk factors and following clinical guidelines, since a delayed diagnosis of PE is associated with increased mortality.