The significant role of academic writing and research in higher education is its contribution as the largest sources of scientific information. There are various kinds of academic writing, as for undergraduate university students, a thesis is one of the most important task to finish their education program and contribute their knowledge. However, writing an undergraduate thesis tend to be challenging task, as it requires a good understanding of the topic and good writing skills. Therefore, the researcher aims to focus on researching the difficulties in undergraduate thesis and the factors of the difficulties. This research is conducted using descriptive qualitative research design with 5 students undergoing the task of writing undergraduate thesis as the research participants. The study implemented using interview guide adapted from Cheung (2013) consisting of six questions. The data collected using the semi-structured interview through WhatsApp voice note due to social distancing protocol in the midst of COVID-19. The data analyzed by using qualitative data analysis based on Creswell (2009) which includes data selection, grouping, and organization, generating a description, discussion and drawing conclusion. The result of the study reveals that the student encounters several problems including difficulties in qualitative data analysis caused by lack of information and course about qualitative data analysis, finding relevant literatures caused by lack of availability of related literature, laziness due to revision and different perspective between the advisors, as well as difficulties in specific chapter. In terms of non-linguistic difficulties, the students mostly struggle in content organization, while, linguistic problems occurs in the writing process includes lexical and structure problem but it’s proven to be less problematic. Keywords: Academic Writing, Difficulties, Undergraduate Thesis.