The effects of noise on students’ health, well-being, and learning are of growing concern among both the general public and policy-makers in Europe. Several studies have highlighted the consequences of noise on children’s learning and performance at school. This study investigates the relationship between noise judgment in school goers aged 11–18 and noise measurements aimed at evaluating their exposure at school. For this purpose, a questionnaire was administered to 521 individuals in 28 classrooms in eight schools of four cities in Italy, with different environmental characteristics. Using a Likert-type scale, a selected set of responses related to noise generated an Annoyance Index (AI) score for each student and a classroom median score (MAI). From the noise data acquired, a global noise score (GNS) was assigned to each classroom. A higher AI was found in industrialized areas and among younger students. No significant differences in noise judgment were found by gender. A significant inverse correlation was described between MAI and GNS, thus the better the acoustic quality of the classrooms, the less the perceived noise and annoyance. The results show that noise perception and consequent disturbance are highly correlated with classroom acoustics, and confirm that annoyance represents the most widespread subjective response to noise.