The purpose of this study was to investigate whether student performance in creative thinking could be enhanced through Problem Based Learning delivered online (referred to as PBL online) and critical thinking. Students’ perceptions and adoptions of PBL learning and online learning also were studied. The PBL online model was adopted from the McMaster’s Model, and comprised three major steps: (i) problem posing; (ii) information searching; and (iii) discussion and application of knowledge in solving problems. PBL is operationally defined here as an instructional strategy which focuses on problem solving. Students are faced with real issues which they have to solve through information searching and group discussion online. In this study, students were given physics problems to solve as part of their Modern Physics course. The phases involved were (i) overview of the topic of the lesson; (ii) problem encounter; (iii) problem definition; (iv) exploration; (v) solution; and (vi) reflection. All of these phases were done through the University’s Learning Management System (LMS), which thus acts as the online delivery tool. This study employed a quasi-experimental design based on mixed between-within-subjects repeated measures. The independent variable was the instruction method, either PBL online (experimental) or Traditional method online (control), and the dependent variables were performance in creative and critical thinking. The Torrance Test of Creative Thinking (TTCT) and the Watson Glaser Critical Thinking (WGCT) were used to measure the respective dependent variables. In the TTCT, there are four criteria used to evaluate creative thinking: (i) fluency; (ii) flexibility; (iii) originality; and (v) elaboration. For the critical thinking, five criteria were used: (i) making an inference; (ii) making an assumption; (iii) deduction; (iv) making an interpretation; and also (v) evaluation argument. Additionally, students’ perceptions and adoptions of PBL, as well as online learning, were captured through this study. A total of 102 students from the School of Science and Technology (SST) and the School of Education and Social Development were the subjects of the study. The SST students were science physics students (N = 61), and the SESD students were pre-service science teachers (N = 41). Results of the Mann-Whitney U test and also Independent Sample t-Test showed that there was significant difference in creative thinking in overall for both SST and SESD cohorts in favour of the PBL group. In addition, when the analysis was focussed on the two cohorts (i.e., SST and SESD), there were statistically significant differences observed for flexibility, originality and elaboration also in favour of the PBL group. However, results from the same analyses showed there was, in general, no significance difference for critical thinking for both cohorts. Further analysis identified statistically significant differences for making an inference (in favour of the PBL group) and assumption (in favour of the Traditional group). For the SST students, there were statistically significant differences in making an inference and evaluation argument criteria, in favour of the PBL group. Nevertheless, there were statistically significant differences for assumption, in favour of the Traditional group. No statistically significant differences were noted in any criterion for the SESD group. Students’ perceptions of PBL and willingness to adopt it were positive, even though they reported feeling confused at the beginning of the learning process. PBL was also reported as taking more time and requiring more effort. Nevertheless, students reported managing to build their capacity for self-directed learning and improving soft skills (i.e., communication, managing their learning timetable, finding relevant and valuable knowledge online, etc.). In the case of online learning, the students felt that they had learned how to get much more information online, and how to critique such information. Students’ readiness to use online learning was encouraging, and it provided at least basic experience on courses delivered through online learning. However, the Internet access needs to be adequate to ensure that online learning operates satisfactorily. Important findings were derived from this study. First, the results from this study suggest that PBL online enhances of Malaysian tertiary students’ creative thinking for both science physics students and pre-service science teachers. Second, PBL online also is capable of having a positive impact on students’ critical thinking for certain criteria, but this would be fostered by a whole programme approach rather than delivery via a single course. Third, students’ acceptance and perceptions of PBL and online learning were positive and encouraging, this despite encountering some issues technical during the intervention.