Problem-based learning (PBL) is a modern strategy used in many higher education institutions. The coronavirus pandemic in 2020 urged universities and other educational institutions around the world to close, leading to the shift to online learning as an alternative in order to overcome delays in the education process. The Faculty of Basic Medical Sciences (BMS) at the Libyan International Medical University (LIMU) has adopted the PBL method as a key element in its teaching strategy. The Faculty started a trial for online PBL sessions during the lockdown period to evaluate the student experience at BMS. Here, we used a binary questionnaire where responses of 293 students were anonymously collected. Overall, there was a positive response of about 76%. Each of the questionnaire elements scored at least 73% which reflects general satisfaction with the online PBL experience. However, there seemed to be considerable variation in the responses of the different year groups. First year students reported the highest overall positive response on the experience whereas third year students were overall less satisfied. In addition, this variation in responses was more pronounced when students were asked about the organisation of the session and problems with internet connectivity. This may be due to the fact that the more senior year groups were interviewed first and there was a continuous adjustment of the online PBL strategy throughout the time for this trial. Our study also showed that among the different online PBL aspects surveyed in the questionnaire, the clarity of instructions was the most important element determining the effectiveness of online PBL. Overall, this questionnaire shows that online PBL can be a decent alternative to traditional PBL during crises.