Exposure to particulate matter (PM) has been associated with several adverse health outcomes. Studies indicate that children may be exposed to much higher concentrations of PM at school than in other environments. There exists very little data on the deposited dose of PM while children attend classes. This study was carried out in a school located near an industrial complex in Portugal and attended by children aged 3–12 years. Indoor PM10, PM2.5 and PM1 were measured over two seasons in classrooms representing different school year groups. Particle deposition fractions in the respiratory tract, as well as the deposited doses, were calculated using the Multiple-Path Particle Dosimetry (MPPD) and the Exposure Dose Model (ExDoM2). Both models were implemented assuming an 8-h exposure scenario to represent the school day. In general, differences in PM concentrations were observed depending on room occupancy periods and season. The highest mean PM2.5 concentration was recorded in winter when the classroom was vacant (23.7 ± 20.5 μg m−3), while the highest mean PM10 level was observed in spring during school hours (61.7 ± 24.2 μg m−3). Regardless of the dosimetry model, the highest deposition of PM10 and PM2.5 was in the upper region, while the lowest was in the tracheobronchial (TB) region. The results indicate that deposited dose and deposition fraction in spring may be more harmful to pupils’ health than in winter. PM10 presented the highest doses, ranging from 54.2 to 128 μg and from 83.9 to 185 μg, according to MPPD and ExDoM2 estimates, respectively.