The present study aimed at investigating the effectiveness of a cooperative inquiry- based program on developing first year EFL secondary students' reading comprehension and reflective thinking skills. The study adopted the quasi- experimental design. Two classes in Meit Abo Arabi Secondary School were distributed into two groups, control and experimental. One class served as the experimental group (n=30) who received instruction through the cooperative inquiry- based program, whereas the control group (n=30) was taught via the Teacher's Guide of the Ministry of Education. The experiment lasted for eight weeks. The instruments of the study included a reading comprehension skills test, and reflective thinking skills scale. They were approved by a panel of jury. To determine the necessary reading comprehension skills to be developed through the program, a checklist was designed and the reading comprehension skills were approved by the jury members. Based on these reading comprehension skills, a reading comprehension test was developed and used as a pre-posttest.  To measure the students' reflective thinking levels, reflective thinking scale was adopted and approved by the jury members. Results indicated that there was a statistically significant difference between the mean scores of the experimental group and that of the control one on the post- administration of the reading comprehension test favoring the experimental group. Moreover, results revealed that there was a statistically significant difference between the experimental group and that of the control one on the post-administration of reflective thinking scale favoring the experimental group. As such, it was concluded that the cooperative inquiry -based program had a positive effect on developing first year EFL secondary students' reading comprehension and reflective thinking skills.