Objectives: To determine the association of students’ perception of schooling with externalizing/internalizing scores; and to examine the different perceptions related to truancy. Methods: A total of 373 predominantly 16 year-old students attending three high risk schools in Pudu, Kuala Lumpur completed the questionnaires on schooling variables (four items) and externalizing/internalizing syndromes (Youth Self-Report, 112 items). Results: Certain negative perceptions (uncertainty of the schooling purpose, thinking schooling as time wasting) were significantly associated with higher internalizing (p<0.05), externalizing (p<0.005) and total problem (p<0.005) scores. Truants were significantly associated with disliking school (OR=2.52, 95% CI=1.01-6.20), lower educational goals (OR=2.03, 95% CI=1.18-3.49) and uncertainty of the schooling purpose (OR=3.14, 95% CI=1.47-6.67). Among truants, those who thought schooling as time wasting scored significantly higher on externalizing (p<0.005) and total problems (p<0.005). Conclusions: Certain negative perceptions of schooling are associated with self-reported emotional/behavioral problems and truancy. Positive schooling experience may correct schooling misperceptions and solve related emotional and behavioural problems.