PeerWise is a novel, freely available, online pedagogical tool that allows students to create and deposit questions for peer evaluation. A participatory learning approach through this web-based system was used to motivate and promote a deep approach in learning nervous system by 124 second year MBBS students at Cyberjaya University College of Medical Sciences. PeerWise was introduced to the students as an optional component within the nervous system course syllabus. The students were asked to create at least two multiple-choice questions (MCQs) covering different aspects of the syllabus components and to evaluate four MCQs from other students throughout the 5-week duration from December 2013 to January 2014. It was mandatory that the students write, answer and explain their MCQs. It was also essential that they answer, rate and give constructive comments on the MCQs written by their peers. The study reveals that the students were active participants and created a large question bank based on the course syllabus with variable quality. Spearman correlation analysis was performed and shows correlation coefficient values falling in a range between 0.634 to 0.739 indicating moderately strong relationship of PeerWise activity with the mark scored in the course. This study reveals that PeerWise is a feasible and large-scale team-based learning tool as the students improve their learning through peer support, analytical and critical thinking as well as personal reflection.