In an extension of research examining student-centered pedagogy, the present case study examined how at-risk students used Alien Rescue, a problem-based learning (PBL) software program for middle school science. Twenty-nine participants were observed and interviewed over the twelve class days in which they were engaged in Alien Rescue. Students' reactions to the software, their problem-solving strategies, and their interactions with classmates were explored. Observations suggest that prior academic performance is the most important characteristic in explaining differences in how these students performed in this PBL unit. Recommendations for the effective use of PBL with at-risk students are made.