Developing higher-order critical thinking skills as one of the central objectives of education has been recently facilitated via software packages. Whereas one such technology as computer-aided argument mapping is reported to enhance levels of critical thinking (van Gelder 2001), its application as a pedagogical tool in English as a Foreign Language (EFL) settings has been rarely explored. In addition, the literature fails to acknowledge whether having the basic skill of representing an argument diagrammatically even with paper and pencil can lead to similar results. That being the case, this study was conducted with the aim of comparing the impact of teaching argument mapping via "Rationale"™ software versus "paper and pencil" on Iranian EFL majors' critical thinking skills development. To this end, 180 EFL participants were screened into low and high levels of reading proficiency based on their scores on a sample reading proficiency test. Next, they were randomly assigned to two experimental and one comparison groups. During 12 sessions, the experimental groups were provided with argument mapping instructions while the comparison group received a conventional reading instruction. All participants were pre- and post-tested with the California critical thinking skills test (CCTST). Results suggested that students in the software group significantly outperformed those in the paper and pencil group on overall CCTST and the sub-skills of inference and inductive reasoning. They also scored significantly higher on all tests compared to the comparison group. However, participants' level of proficiency as well as sex did not show any significant effect on their performance on overall CCTST and its sub-skills.