Background: This study describes the perceived impact of H1N1 influenza and the adoption of the recommended measures to address the pandemic in schools. Methods: A cross-sectional self-reported survey was conducted in 433 schools in Barcelona addressed to the school principal or the H1N1 influenza designated person. A descriptive analysis was performed, stratifying by educational level and type of school. A logistic regression analysis also was conducted. Results: Around 70% of the respondents reported that there had been H1N1 influenza cases among students, being this percentage significantly higher among those schools offering primary education (74.4%) (p < 0.05). The main measures (single-use paper towels, availability of sanitizer solutions and 15 minutes ventilation per day of enclosed spaces) were implemented in most of the centers. However, the correct adoption of the main measures took place in around 30% of the schools, being the percentage lower in those offering only secondary education (Odds ratio [OR]: 0.518; 95% confidence interval [CI]:0.272-0.986) and those located in medium (OR: 0.438, 95% CI: 0.234-0.811) or low socioeconomic status (SES) districts (OR: 0.321, 95% CI: 0.159-0.649). Conclusions: Despite the climate of social alarm, the perceived impact of H1N1 influenza in most schools was moderate. In future potential threats, the educational level and the SES of the school should be considered, especially when measures requiring purchasing any product are recommended but not provided.