Introduction Medical education involves training necessary to become a physician or a surgeon. This includes various levels of training like undergraduate, internship, and postgraduate training. Medical education can be quite complex, since it involves training in pre-clinical subjects (anatomy, physiology, biochemistry), the para-clinical subjects (microbiology, pathology, pharmacology, and forensic medicine), and a discrete group of clinical subjects that include general medicine, surgery, obstetrics and gynaecology, ear, nose and throat specialization, paediatrics, cardiology, pulmonology, dermatology, ophthalmology, and orthopaedics, and many other clinical specializations and super specialities (cardio-thoracic surgery, neurosurgery, etc.). Training medical students involves both classroom teaching and practical applications. Classroom teaching is usually confined to didactic lectures, where the teacher unilaterally disseminates the information. This kind of teaching was recently noted to be not very effective in producing better quality medical graduates. The present study aims to introduce problem-based learning (PBL) to teach microbiology to undergraduate medical students and evaluate their perception towards such type of learning. Methods A total of 159 students were included in the study. An informed and oral consent was obtained from each participant, and the study was approved by the institutional ethical committee. All the students included in the study were grouped into 14 groups of 11-13 students. Students were carefully grouped ensuring that each group had a good mix that included different levels of achievers. Students were given a detailed introduction to the exercise before they started it. A questionnaire that consisted of 11 points was given to the students and they were asked to give feedback (strongly disagree, disagree, agree to some extent, agree, strongly agree) both on the functioning of PBL and the tutor performance during PBL. Results The study included a total of 159 students. Among the study participants, 55 (35%) were male and 104 (65%) were female. There was a positive response towards PBL being instrumental in improving cognitive skills as evidenced by the results (females (59%) and males (29%)) (p=0.191). We found that 61% females and 30% males felt that PBL was the best learning technique, as compared to traditional teaching (p=0.241). Most students were happy with the number of students in a group (females (63%) and males (34%)), but a few students felt that there would have been an improvement in the learning process if the groups were smaller (<10 students) (p=0.239). A positive response was given by the students regarding the feedback encouragement provided by the tutor (females (43%) and males (27%)) (p=0.253). Tutor evaluation by the students revealed some interesting observations, which include an agreement by most students that the tutor had completely avoided traditional teaching (females (55%), males (32%)) during the PBL sessions (p=0.001). Conclusion Most students liked PBL as it encouraged group discussions and presentations, which helped in retaining information and improving cognitive skills.