Introduction: The purpose of this research was to analyze the relationships between pharmacists knowledge, work environment, and self-efficacy to their compliance level with the COVID-19 health protocols. Methods: This cross-sectional study was designed with descriptive correlational data collection using a questionnaire. Simple random sampling was used to choose the participants who are pharmacists from the Special Region of Yogyakarta’s Province. The demographic characteristics of the respondent were presented descriptively. The demographic characteristics of the respondent were presented descriptively. A statistical test was used to assess the correlation between compliance level vs each of the three factors from the Social Cognitive Theory. Results: A total of 262 pharmacists were selected with data collection using a questionnaire. Most of them were in a medium level of compliance (65.6%), while only 19.1% in a high level, and the 15,3% in a low level. Correlation values of 0.463 and 0.409 between variables measuring the organization’s environment and self-effciacy were found to be statistically significant at the p value <0.05. Meanwhile, there was no statistically significant relationship between knowledge and compliance (p>0.05) with correlation value was 0.054. There is good compliance to the COVID-19 health protocols among community pharmacists in the Special Region of Yogyakarta. Conclusion: These findings indicate that improving factors from pharmacy organization-environmental and self-efficacy of pharmacists may improve community pharmacists level of compliance to COVID-19 health protocols in pandemic era.