Acute non-traumatic headache is a frequent complaint in emergency primary care. In the majority of cases, the cause is a primary headache, which can be invalidating, but should not lead to additional investigations. Secondary headaches are rare but their diagnosis is essential to avoid potentially lethal consequences. In practice, a primary headache may be difficult to differentiate from a secondary headache, especially if the initial management does not follow a systematic approach. We have adapted evidence-based guidelines to improve the diagnostic management of patients presenting acute headache. We propose an algorithm that facilitates the systematic screening of alert signs with a focused patient history and clinical exam. In the presence of red flags, appropriate complementary exams are needed to rule out a secondary headache.