Thesis writing is the culmination of earning a degree. To produce a thesis, the students need to undergo processes in the course of immersion in these stages, difficulties that arise may either hinder or motivate them to finish their respective researches. This qualitative paper delved into the challenges experienced by the students in writing their undergraduate thesis through an analysis of the reflections/narratives submitted by students currently enrolled in thesis writing. During the end of the semester, the students were requested to write a short reflection regarding their difficulties in thesis class. The data that were culled were analyzed using thematic analysis. Similar data were clustered into themes. Results revealed that students had difficulties in formulating their research problem, writing their review of related literature, sampling of their respondents, developing the research instruments, transcribing interviews, video production delays are among others. They also had problems in coordination, plagiarism processing, and other difficulties such as time constraints, absence of research partners, personal issues, and other conflicts. Further, this paper explored approaches to assist the students in overcoming such challenges.