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The aim of the study was to examine the effect of the perceptions of students about classroom learning environment on their academic achievement at secondary level in the Mathematics classrooms. The participants were selected from the secondary and higher secondary schools located in Tehsil Rawalpindi and Islamabad (Federal Area), Pakistan. Twenty four schools were selected randomly. A total of five hundred sixteen students of 10th grade studying Mathematics in twenty seven classrooms, were included in the sample. Classroom Environment Instrument (Personal Form) was used to measure the students' perceptions after translating it into Urdu for Urdu medium schools. The pilot testing was carried out before the actual application of this instrument. The reliability of the instrument was determined by the use of Cronbach Alpha which was found as 0.85. The marks obtained by students in the subject of Mathematics in annual examination in 10th grade conducted by both BISE Rawalpindi and FBISE Islamabad were taken as achievements in Mathematics. The data was analyzed using multiple regression, Pearson r and ANOVA to find out the effect of perception of students about classroom learning environment on their academic achievement. The results of study revealed that the subscales, `Involvement', `Personal relevance', `Emphasis on understanding', were major predictors contributing towards classroom learning environment and students' academic achievement whereas subscales `Investigation' and `Autonomy' have negative effect on students' academic achievement. The researcher recommends that active involvement of the low achievers may affect their learning more positively.