The aim of this study was to examine the effects of using inquiry-based learning on students' critical thinking skills. A quasi-experimental design which employed time series design with single group participants was used. A total of 20 EFL undergraduate students who took advanced writing skills course were selected using comprehensive sampling method. Tests, focus group discussion, and student-reflective journal were used to gather data on the students' critical thinking skills. The participants were given a series of three argumentative essay writing pretests both before and after the intervention, inquiry-based argumentative essay writing instruction. While the quantitative data were analyzed using One-Way Repeated Measures ANOVA, the qualitative data were analyzed through narration. The findings of the study revealed that using inquiry-based argumentative writing instruction enhances students' critical thinking skills. Therefore, inquiry-based instruction is suggested as a means to improve students' critical thinking skills because the method enhances students' interpretation, analysis, evaluation, inference, explanation, and self-regulation skills which are the core critical thinking skills.