Multimedia-supported e-learning is considered useful as it can offer an enjoyable independent learning experience to learners. However, the effectiveness of e-learning for self-regulated science learning is still inconclusive. This study aimed to explore primary school students' perceptions and experiences of self-regulated science learning in a multimedia-supported e-learning environment. A total of 11 classes from grades 3 to 6 from four Hong Kong schools participated in this study. All e-learning lessons were observed, and 33 (3 from each class) were interviewed using cognitive walkthroughs of how they made use of the multimedia resources and system tools, scaffolds, or prompts to direct their own learning in each of the three self-regulated learning phases (forethought, performance, and reflection). Results revealed that the combined use of the discussion forum and statistics table seemed to facilitate the students' diagnosis of their prior knowledge of natural phenomena in the forethought phase. In the performance phase, the students mostly enjoyed learning with the graphic data, animations, and/or simulation experiments. Some perceived the prompts or tools from the e-learning system as useful for operation and science learning. In the reflection phase, the students self-assessed their learning using quizzes with emoticons as positive feedback which seemed to increase their enthusiasm for learning science. However, not all students were able to effectively use the system tools or prompts, to keep focused self-discipline, or to achieve deeper science learning without the teacher's guidance. Hence, this study suggests providing more opportunities for students' exposure to e-learning resources, while at the same time assisting them in the use of digital tools or resources, in adjusting their learning strategies, and in internalizing scientific ideas and inquiry processes so as to ensure more effective self-regulated science learning.