ABSTRACT Nidar Velayati, 2016. An Analysis of Students’ Critical Thinking Skills in reading: The Application and Difficulties. A Qualitative Research at Ar- Raniry State Islamic University. Thesis, Graduate Program in English Language Education of Syiah Kuala University. Advisors: (1) Dr. Asnawi, S. Pd., M. Ed., (2) Dr. Siti Sarah Fitriani, S. Pd., M.A. Keywords: Critical Thinking, Reading This study aims at investigating types of critical thinking skills used by undergraduate students in reading comprehension and the problems faced by them in using it in reading. The skills include interpretation, analysis, evaluation, inference, explanation, and self-regulation. The subjects of this study was students in second year grade of Ar-raniry State Islamic University, Banda Aceh. This qualitative study collected data through interview and questionnaire. The questionnaire were analyzed quantitatively to find out types of critical thinking skills used by students in reading comprehension. The audio recordings from the interview were analyzed qualitatively to find out the problems faced by low-score students in using critical thinking skills in reading. The results from the questionnaire indicate that inference is the critical skill mostly used by students in reading (15% always and 39 % often). Meanwhile, self-regulation was the least skill practised by students in reading comprehension. It was evidenced by the result of questionnaire that among six critical thinking skills which always used by students, only 5% of them did self-regulation as a frequent skill in comprehending reading. In addition, personal interview from five students who got the lowest score in critical thinking ability questionnaire indicated that students practiced rarely had made critical thinking difficult for them. The other problems found were lack of language mastery, implied meaning, background knowledge, repetition and lack of vocabulary. Among six problems discovered above, lack of practicing, background knowledge and language mastery had made the students felt that critical thinking was difficult to be done.