The study intended to explore the students’ perceptions and problems of the implementation of blended learning in their EFL courses. Eight students at UIN Walisongo in Semarang, were involved in this study. The study used a qualitative method with a case study design using semi-structured interview as data collection methods. The data collected was analyzed using thematic analysis. The students’ perceptions were examined in in three dimensions namely learner dimension, instructor dimension, and course dimension. The findings revealed that the majority of students perceived positively both the online and face-to-face modes used in their blended EFL courses. Blended learning brings some benefits in the forms of being reachable at any time, being flexible, providing comprehensive and needed learning materials, encouraging students to become independent learners, improving students’ communication and learning interactions, and saving energy. The students reported that internet connection problems, online technical problems, and ineffective online learning modes were their main problems in implementing blended learning. Furthermore, the study revealed that perception of face-to-face activities was higher than online activities, indicating that students preferred face-to-face learning mode in their blended EFL courses.