We developed, validated, and tested a tool in Mexico to assess the management of student and teacher health and safety, environmental protection, and community safety in high school science laboratories. Schools require such an instrument in order to capture and proactively identify opportunities for safety improvement. We developed a checklist by reviewing and adapting different sources. It can be used to evaluate a school’s management approach using a composite indicator, the Health, Safety, Civil, and Environmental Protection Management Indicator: IHSCE. The IHSCE comprises four sub-indicators: (1) health, safety, civil, and environmental policies; (2) management of chemicals; (3) facilities, safety, and emergency equipment; and (4) teacher training. The IHSCE tool was validated and tested in 41 high schools in the state of Sonora (Mexico). The IHSCE sub-indicator rankings ranged from medium to low in the science laboratories of schools in the capital of the state and in regional high schools. However, regional high schools had significantly lower levels in two IHSCE sub-indicators: the facilities, safety, and emergency equipment sub-indicator and the teacher training sub-indicator. The tool consists of a checklist that is flexible and comprehensive. Its use revealed differences in high school science laboratories and identified opportunities for the reduction of health and safety hazards in school facilities and communities and in the surrounding environment.