Significant improvement has been achieved in diagnostic accuracy, validation of probability scores, and standardized treatment algorithms for patients with suspected acute pulmonary embolism. These developments have provided the tools for a safe and cost-effective management for most of these patients. In our experience, however, the presence of medical myths and ongoing controversies seem to hinder the implementation of these tools in everyday clinical practice. This review provides a selection of such dilemmas and controversies and discusses the published evidence beyond them. By doing so, we try to overcome these dilemmas and suggest pragmatic approaches guided by the available evidence and current guidelines.