The researcher is aimed to find out the factors that affect EFL learners’ listening comprehension difficulties. The sample was taken by 15 students from 4th semester in one of the private universities in Central Java. The technique that has been used in this research to find the sample is by using simple random sampling. The researcher used mixed method in this study. The data collection used in this research are questionnaire and interview. The analysis technique used in questionnaire is using cross-tabulation, while the interview used data reduction, data display and verification. The results revealed that the factors affecting EFL learners’ listening comprehension difficulties are divided into 6 factors, the first and the second factors is come from the speaker, it is the unclear pronunciation which is around 41% answered from the students and the unfamiliar accent of the speakers which is around 35% answered from the students, the third one is the lack of listening strategy by the listener which is around 20% answered from the students. The next factor is the noises from the surrounding of the listener which is around 30% answered from the students, next is a physical setting with all kinds of setting that needed in listening, from the equipment and its quality which is around 26% answered from the students and the last is the psychological state, the nervousness and confidence of the students, but by looking at the findings in interview, this factors is not really affects the students’ difficulties in listening comprehension. The conclusion in this study is there are six factors affects EFL learners’ difficulties in listening comprehension, there are unfamiliar accent, unclear pronunciation, lack of listening strategy and, noises, physical setting, and psychological state.