It is mandatory that healthcare workers wear personal protective equipment (PPE) while caring for COVID-19 patients. Studies have shown that wearing PPE for a prolonged time may lead to symptoms of physical discomfort including headache. The aim of this study is to assess the prevalence and association between prolonged use of PPE and headaches. This was a cross-sectional study. A convenience sample of healthcare workers who worked with COVID-19 patients in clinical settings was recruited. The data were collected through an electronic survey shared as a link through social media. This study included 1060 participants, 753 (71%) female and 307 (29%) male. Participants were divided into two groups. Group A had 628 (60%) participants who did not have chronic headache before the COVID-19 pandemic, while Group B contained 432 (40%) participants who had a previous chronic headache. Headaches differed significantly between Groups A and B in frequency, type, location, and quality during the COVID-19 period. The analysis found a significant relationship between duration of PPE use and headache occurrence. The significant relationship between the duration of PPE usage and headache occurrence among healthcare workers should be considered when refining policies and procedures regarding prolonged PPE use.