Background Online courses that utilize problem-based learning (PBL) are widely recognized as an effective educational method that blends self-directed learning with collaborative problem-solving. Aim The aim of this study was to evaluate the satisfaction of students from the Faculty of Basic Medical Sciences (BMS) at Libyan International Medical University (LIMU) with an online PBL course during the coronavirus disease 2019 (COVID-19) pandemic in 2020. Method This is a cross-sectional study performed during the COVID-19 pandemic in 2020, involving a total of 293 students from four different classes of Faculty of BMS. Each online PBL session ran for 2 hours and was arranged independently for each year group. Students had access to a seven-closed-question questionnaire for a few hours after the end of the session. The questions were of three different categories. The first category was related to the online organization of the session, tutor control, and instructions provided in the applied Modular Object-Oriented Dynamic Learning Environment (Moodle). The second category involves questions related to online communication problems, the facility of the Google Hangouts application used, and the time allocated for the session. The third category was the cooperation of the PBL group. The student was asked to answer agree or disagree for each question. If the student did not choose one of the answers, his response was recorded as (no response). The scores of (agree), (disagree), or (no response) for each student were transferred to a Microsoft Office (2021) Excel file and were displayed as frequency and percentages. A two-way analysis of variance without replication was performed to analyze the differences in student responses across various groups using Excel statistics. The proportion test was utilized to determine whether the proportion of positive responses (agree) in any group significantly differed from a specified level of 0.75 (75%). The acceptable proportion of no response was set at 0.2 (20%). The significant level was set at p-value less than 0.05. Results For the first category, the highest level of student satisfaction (79.9%) was associated with Moodle instructions, followed by tutor control (79.5%), and online organization (72%). However, students in the third year of medicine demonstrated significantly lower satisfaction with online organizations compared with other groups (62.3%, p < 0.05). For the second category, all groups, except first-year medicine students, reported significantly low satisfaction with online access (58% p < 0.05). All groups expressed satisfaction with the time allotted for the session (74%) and the online Google Hangouts application used (71%), except for third-year medicine students, who exhibited a notable level of dissatisfaction with the use of online Google Hangouts application (7%, p < 0.05). Lastly, the third category focused on group cooperation and reflected an overall student satisfaction rate of 80%. Conclusion BMS students responded positively regarding their first online PBL session during the COVID-19 pandemic. The study displayed that the availability of online communication, the clarity of instructions, good session organization, and control are important factors that will determine the effectiveness of online PBL.