In 2020, the COVID-19 pandemic affected formal and informal education programs in the USA. The pandemic had a devastating impact on programs that required a dedicated physical space and in-person laboratory research. The distinguishing feature of New Hampshire Academy of Science (NHAS) programs is the participation of secondary school students in STEM research projects that emulate university-level research. Moving to a remote format presented various challenges. In this case study, we describe and discuss our experiences transforming a summer STEM research program for secondary school students from on-site and in-person to a remote platform, providing details of the planning phase, the logistics of maintaining the quality of the students' research, and the results of internal and external evaluations. Of the 33 students who participated, 32 completed all central elements of the program, and 25 went further and submitted summary papers and presented their research at the remote annual meeting of the American Association for the Advancement of Science. External evaluation found that students saw their work as similar to that of professional scientists, and perceived themselves to have gained proficiency in the use of scientific techniques and instrumentation. Students expressed they missed elements of in-person lab work including social interactions.