In this study we examined the effectiveness of self-regulated learning (SRL) training in facilitating college students’ science learning with hypermedia. Sixty (N = 60) undergraduate students were randomly assigned to either a training condition or a control condition and used a hypermedia environment to learn about the circulatory system. On Day 1, all participants were administered a pretest and a self-report measure of SRL. On Days 2–4, participants in the experimental group underwent 3-day training on the use of specific, empirically based cognitive and metacognitive SRL processes (e.g., judgment of learning, making inferences) designed to foster their conceptual understanding; control students received no training. Three weeks later (on Day 5), all participants were administered a pretest on the science topic and a self-report measure of SRL, and then used a different version of the system to learn about another science topic (i.e., the central nervous system). Verbal protocol data were collected from both groups on Days 2–5. Overall, there were no significant differences on several learning outcome measures between conditions. However, those in the training condition remembered significantly more declarative knowledge of cognitive and metacognitive strategies. Lastly, think-aloud protocol data showed significant differences in the use of the SRL processes immediately following training, but not following a 3-week interval on a hypermedia transfer task.