The research that successful learning can be achieved by self-management skills or high learner autonomy has drawn the attention of many researchers. Due to the development of technology in recent years, the effect of an electronic form of portfolio called e-portfolio towards language learning has been further expected. The purpose of the present study was to investigate how the implementation of e-portfolio can improve the students’ learner autonomy and how the students’ perception on e-portfolio can change over the academic year. The study participants were 37 first-year university students who took a general English course at a private university in Tokyo. The online surveys were administered at the start and end of one academic semester in order to compare the score in their learner autonomy and inspect their perception on e-portfolio. The results showed that the students’ learner autonomy slightly increased while the perception on e-portfolio was overall positive. By being able to manage their own learning, the present study revealed that the use of e-portfolio was substantially helpful for students to become more autonomous in language learning. The findings of the present study could also be applicable to a variety of instructional settings.