Background Healthcare workers in frontline during the coronavirus 19 disease (COVID-19) pandemic are mandated to wear specific personal protective equipment (PPE) including high filtrating masks and/or eye protection during extended period of time. Compressive headaches secondary to PPE use including N95 masks have been reported. We aim to describe subtypes of headache related to PPE use in our hospital in Casablanca and working condition factors associated with it. Methods We conducted a cross-sectional study among healthcare workers in frontline at Cheikh khalifa International University Hospital, using an online questionnaire. We collected demographic data, comorbidities and previous headaches history. Data about working conditions during pandemic, type and duration of PPE use were described. We calculated the prevalence of De Novo or an aggravated headache among healthcare workers. We studied correlations between PPE related headaches and working conditions and trends in PPE use during the pandemic. Finally, we described the overall discomfort related to PPE use. Results A total of 155 healthcare workers responded to the questionnaire. The N95 masks were the most used type (95.5%) associated with an eye protection in 61.3%. The overall prevalence of headache related to PPE was 62%. It was experienced De Novo in 32.9%, while it was an aggravation of pre-existing headache in 29%. Working more than 8 hours per shift during the pandemic was correlated to De novo headache (p = 0.008). The profession of doctor and working more than 12 hours per shift were correlated to aggravated headache (p = 0.02, p = 0.023). Healthcare workers experienced moderate discomfort, blurred vision and reduced concentration. They judged their professional performance mildly reduced by the use of PPE. Conclusion The increased use of PPE, especially high filtrating masks during the COVID-19 outbreak is responsible for generating headaches in healthcare workers on frontline either De novo or as an aggravation of pre-existing one. Working conditions have the greater impact on generating these types of headaches more than any pre-existing comorbidity. These findings should be considered to accommodate health care professionals to increase efficacy and adherence to protective measures during pandemic.