Background The COVID-19 pandemic led to an unprecedented increase in the use of personal protective equipment (PPE) among medical personnel. The goal of this study was to determine the risk factors and frequency of PPE-induced headache during the COVID-19 pandemic. Methods From January 25 to March 1, 2021, an anonymous online survey was undertaken in the Baltic states. Results In total, 2132 individuals participated. 52.3% experienced a PPE-induced headache. Usual onset time was between 2–3 h, lasting up to 1 h after PPE removal. The most common localization was in temporal and frontal regions. Headache usually occurred 2 to 3 days per week with an average pain score of 5.04 ± 1.80 points. Higher risk was associated with discomfort/pressure OR = 11.55, heat stress OR = 2.228, skin conditions OR = 1.784, long PPE use (duration 10-12 h) OR = 2,18, headache history prior PPE use OR = 1.207. Out of 52.3% respondents with PPE-induced headache, 45.5% developed de novo headache, whereas 54.5% had headache history. Statistically significant differences of PPE-induced headache between respective groups included severity (4.73 vs 5.29), duration (≥ 6 h 6.7% vs 8.2%), accompanying symptoms (nausea (19.3% vs 25.7%), photophobia (19.1% vs 25.7%), phonophobia (15.8% vs 23.5%), osmophobia (5.3% vs 12.0%)) and painkiller use (43.0% vs 61.7%). Conclusions Over half of the medical personnel reported headache while using PPE. The risk was higher in individuals with headache history, increased duration of PPE use and discomfort while using PPE. Predisposed individuals reported PPE-induced headache which persisted longer, was more intense and debilitating than in the respondents with de novo headache.