Pakistan is highly exposed to climate-induced disasters, especially floods. Flooding history shows that educational establishments have been disproportionately hard-hit by flooding events. In Pakistan, school safety and preparedness is still a choice, rather than a mandatory requirement for all schools. But schools in Pakistan do have a responsibility to keep safe the students in their care, especially during and after the catastrophic events. This implies the need to maintain the environment in and around school property, so as to minimize the impacts of floods and to have the mechanisms in place to maximize a school's resilience. This study examined the emergency preparedness activities of 20 schools in four districts of Khyber Pakhtunkhwa Province that had recently been severely affected by floods. Through face to face interviews and a structured questionnaire (n = 100) we collected data on the four pillars of emergency preparedness: emergency planning, preparation measures, safe school facilities, and hazard education and training. The study revealed that the majority of the sample schools had experienced more than one natural hazard-induced disaster, predominantly flooding, yet despite this had not undertaken adequate emergency preparedness activities. There are particular gaps with regard to plans for students with disabilities, the continuity of school operations after a disaster, the presence of maps to identify evacuation routes, the availability of emergency equipment and resources, disaster preparedness guidelines, and psychological first aid and crisis counseling. The strengths, weaknesses, opportunities, and threats analysis that our researchers carried out indicates that, although schools in the survey have taken many steps towards flood preparedness, many weaknesses still exist and there remain significant opportunities to strengthen the preparedness level of many schools. The goal of this study is to inform policy decisions that improve school safety in Pakistan and to suggest the priority areas for future school disaster preparedness and management efforts.