This study aimed to investigate the relationship between rosacea and headaches, focusing on different subtypes, as well as the associated clinical features and triggering factors. In this prospective study, 300 patients diagnosed with rosacea and 320 control subjects without rosacea or any connected mast cell activation illness were included. Patients with rosacea were assessed by a dermatologist according to the 2019 updated rosacea classification (ROSCO panel). Accordingly, patients were classified based on their predominant rosacea subtype as follows: erythematotelangiectatic (ETR), papulopustular (PPR), or phymatous (RhR). Patients experiencing headaches were assessed using the International Headache Classification. Headaches were categorized as migraine, tension-type headaches (TTHs), secondary types (STHs), and cluster-type headaches (CTHs). The ratio of headache was 30.3% in the rosacea group, which did not show a significant difference compared to the control group (30.3% vs. 25.0%, p = 0.138). In 81.3% of rosacea patients with headaches, headache onset occurred after the diagnosis of rosacea. The rate of patients with headaches was higher in the ETR group compared to the PPR and RhR groups (35.2% vs. 16.2% vs. 23.1%, p = 0.007, respectively). In terms of headache subtypes, the rates of patients with migraine and STHs were higher in the ETR group compared to the PPR and RhR groups, while the rate of patients with TTHs was higher in the RhR group. A positive correlation was found between rosacea severity and migraine severity (r = 0.284, p < 0.05). Among the triggering factors for rosacea, only sunlight was found to be associated with headaches. Lower age, female gender, and moderate to severe rosacea severity were identified as independent factors increasing the likelihood of headaches. A significant portion of rosacea patients experience headaches. Particularly, different subtypes of rosacea may be associated with various types of headaches. This study, highlighting the connection between migraine and ETR, is a pioneering work that demonstrates common pathogenic mechanisms and potential triggers.