This study aims to investigate whether deliberate computer-assisted argument mapping practices are effective for promoting pre-service teachers' critical thinking and helping them make better arguments over time within a fourteen-week online undergraduate course. A design-based study nested within a factorial repeated measures design with a single group of pre-service teachers is conducted to fulfill this aim. Thirty-eight junior pre-service teachers, enrolled in an early child-hood education department at a middle-sized university in Turkey, were recruited for the study. The primary data collection tool in this study was argument maps generated by pre-service teachers on various pedagogical and authentic cases by using an online free tool. Assessing critical thinking and the quality of argument maps, two different types of rubrics (holistic vs analytic) that appear to have the face and construct validity were located. Experimental evidence supports statistically significant progress in pre-service teachers' critical thinking scores after engaging in deliberate computer-assisted argument mapping practices regularly as homework assignments. There is also sufficient evidence to suggest a moderate relationship between critical thinking and argument quality. The study advances our knowledge of engaging in deliberate computer assisted practices to be an appropriate course of action for promoting critical thinking by helping pre-service teachers diagram qualified arguments. It is apparent in this study the success of the use of a computer assisted argument mapping tool for promoting CT depends on to what extend students are engaged in constructing better argument maps with each round of practice and scaffold.