Science, Technology, Engineering, and Mathematics (STEM) instruction in the United States has been a major focus of educational reform since the release of the PISA rankings in 2000, which showed that the U.S. was behind many other countries on the international stage in the areas of Science and Math. Students are also leaving the "STEM Pipeline" at various points in their education and not pursuing careers in STEM. The purpose of this study was to utilize a mixed methods qualitative case study with descriptive statistics methodology design to investigate the perceived impact on student engagement in students who participate in a mentor-facilitated, multi-year science research course at the secondary level. The Student Engagement Instrument (SEI) was used to measure students' cognitive and psychological engagement. One hundred and seven students were surveyed (n=107), with forty-five (45) enrolled in science research and sixty-two (62) enrolled in an advanced-level science course (Honors, AP, and IB). There were no statistical differences found in student engagement between the two groups. Ten (10) students and five (5) educators were interviewed for the qualitative phase of the study. From these interviews, ten (10) areas of cognitive, behavioral, and psychological engagement were identified. These included things like advocacy in learning, community, active learning, and relevance of work. The components of a science research program that contribute to these areas of student engagement were also identified: (1) Ability to select topic of study, (2) Extended course length, (3) Mentorship, (4) Conferences, symposia, and competitions. Lastly, challenges and barriers to implementation were identified by teachers for the creation of new science research programs and the impacts of the COVID-19 pandemic and remote learning were highlighted. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://bibliotheek.ehb.be:2222/en-US/products/dissertations/individuals.shtml.]