This study aimed to assess the present physical environment of the three affected school of Severe Tropical Storm Vinta and the pupils learning behaviour in terms of classroom attendance, initiative to do assignment, class recitation, cooperation in classroom activities during the school year 2018-2019. The respondents of this study were the 378 Grade 4-6 learners from Pendulonan Elementary School, Munai Central School and Lininding Elementary School. For the physical environment the general assessment of the respondents showed that they have impractical school environment both inside and outside the classroom after affected by the TS Vinta. With regards to pupils‟ learning behaviour. the results describes that the pupils do most of the time attending their classes, doing better in the initiative of making their assignments, participative and attentive in the class recitation and showed moderate level of cooperation in classroom activity. The result also reveals that school attendance and physical environment relative to inside the classroom are significantly correlated. This suggests that pupils having lower school attendance could be link to poor classroom learning environment .However, the pupils‟ learning behaviour relative to initiative to do assignment, class recitation and cooperation in class activity are not significantly associated both inside and outside the classroom environment . This result suggests that some of the learning behaviours of the pupils are not interfered by the physical environment of the school.