This study aimed at investigating the effect of strategy-based instruction on undergraduate students' reading performance and reading autonomy in an English for Academic Purposes (EAP) context. Test of English as a Foreign Language (TOEFL) reading comprehension tests and learner autonomy questionnaire in EAP reading were utilized to collect data. The collected data were analysed using two "t"-tests to assess the effect of strategy-based instruction on EAP students' reading performance and reading autonomy. The results of data analysis showed that the students took more advantage of reading strategies instruction on their reading comprehension; therefore, they responded positively to such intervention. However, the desired effect on their reading autonomy was not significant whatsoever. On the other hand, the collected data were analysed using multivariate analysis of variance to examine the interactional effect of the proposed method of instruction on the relationship between EAP students' reading performance and reading autonomy. The results of data analysis revealed that the only significant difference between both groups was in their reading comprehension.