The purpose of the present study was to examine the effect of instruction through debate on male and female EFL learners' reading comprehension. Also, their perception of critical thinking (CT) instruction was investigated. A quantitative research method with experimental pre-and post-tests design was conducted to collect the data. Eighty-eight EFL learners--who were selected via convenience sampling method--were randomly assigned to two experimental groups (22 males and 22 females) and two control groups (22 males and 22 females). Data were analyzed using descriptive and inferential statistics. The Oxford Placement Test (OPT) was administered to choose the intermediate sample. To ensure the homogeneity of the participants in terms of reading skills, the Reading Comprehension Placement Test (RCPT) was conducted. Also, the California Critical Thinking Skills Test (CCTST) and Read Theory Critical Reading Comprehension Test (RTCRCT) were used as pre-and post-tests to measure the students' CT skills. Although the findings showed that debate had a statistically significant effect on EFL learners' reading comprehension ability, the role of gender was not found to be significant. In addition, the results revealed that there was no significant difference between male and female EFL learners' perception of CT instruction. It was concluded that instructing CT skills through debate resulted in a better understanding of the reading texts.