Teaching English using Direct Method (DM), which only uses the target language and refrains from using the learners' native one, does not always seem understandable for some students, especially those who are in the first year of study in a tertiary level context. Responding to such an issue, this study was aimed at investigating students' understanding and perceptions of the implementation of DM in an EFL classroom. This study applied a case study of qualitative research design, where the researcher took one experienced-English lecturer who is an expert in using DM and thirty students of English major in the first year of study. The data of the study were gained through interviewing the lecturer, and questionnaires with open-ended questions distributed to forty-one students. The result of this study showed that the causes of difficulty are lack of vocabularies, infrequent practice, and inability to understand the explanation in a fast tempo, and unfamiliar pronunciation. Moreover, there are three proposed suggestions to effectively implement the DM, namely a lot of exposure, reading the materials before the class is begun, and working in a group consisting of high and low achievers.