The aim of this study is to examine the effect of mobile technology use in university science instruction on students' academic achievement and self-regulation skills. An experimental study is conducted to test the use of mobile in-class interaction system (M-CIS) and to determine the change in students' academic achievement and self-regulation skills in a science class. Motivated Strategies for Learning Questionnaires, Academic Achievement Tests and Semi-structured interview forms are used as data collection instruments. In the data analysis process, descriptive statistics, covariance analysis (ANCOVA), Mann-Whitney U test and content analysis are used. At the end of the study, it is found that the use of mobile technology in science instruction sustained to be effective in increasing students' academic achievement. Besides, the M-CIS provided significant changes in teaching, instruction and learning atmosphere, as well as students' and teachers' affective outcomes.