Introduction: Problem-Based learning (PBL) pedagogy is one of the most significant development in education and has been introduced worldwide into many dental school’s curricula since 1990s. The research that has been carried out on PBL in dentistry especially with application of knowledge in clinical learning is still limited. Aims: The aim of the study was to assess the undergraduate dental students’ perception of PBL implemented during their clinical years and analyse if PBL plays a role in application of their knowledge to improve – diagnostic, clinical reasoning and treatment planning skills. Methodology: Following ethical approval, using purposive sampling, a total of 18 students from fifth year dental undergraduate who attended the PBL sessions were asked to participate in focus group interviews. Transcripts of the audio-recordings were coded and analysed using thematic analysis. Results: The five major themes identified: PBL transition, Clinical learning including diagnostic, clinical reasoning and treatment planning skills, Strengths, Weaknesses and Improvements in PBL process considering positive and negative aspects. Overall, students had positive perception about the PBL process and also agreed that it helps in clinical learning such as diagnostic and treatment planning aspect. Although some concerns were raised such as PBL was stressful, time consuming, difficult to correlate in twinning programme, and complex PBL cases. Conclusions: The implication of this research findings will be useful for PBL and curriculum committee to modify PBL curricula and to develop PBL problems in order to benefit future dental students and also to achieve the intended clinical learning objectives.