Reading comprehension (RC) and critical thinking (CT) are the two basic cognitive skills that should be developed through involving language learners in a carefully planned instruction. Multiple intelligences (MI) instruction may assist learners in developing RC and CT in L2 education. This study probed the effect of MI-based reading instruction on the Iranian EFL learners’ RC and CT skills. In so doing, it compared the effectiveness of an MI-based reading instruction with a traditional one. To this end, 4 intact classes from several English language institutes, comprising 56 Iranian intermediate-level EFL learners, were selected and randomly assigned to MI-based (experimental) and traditional (control) groups. A multiple- choice RC test, a reading summary test, and the Watson-Glaser Critical Thinking Appraisal test were used as the instrumentations to collect data on the participants’ RC and CT. Analysis of covariance revealed a significant effect for the MI-based reading instruction. Furthermore, the RC scores increased more significantly in the MI-based group in comparison to the traditional one. However, the CT scores did not significantly improve in both groups. There was also no statistically significant difference in the CT scores between the two groups after the treatments. Iranian EFL educators are, then, encouraged to develop MI-based lessons and activities for diverse students and take explicit instruction for the enhancement of CT skills in EFL reading courses.