Previously, we described a course-based undergraduate research experience (CURE) for first-year students that featured a unique approach to brain mapping in a model organism (rat). In response to the COVID-19 pandemic, we adapted this course for an online learning environment, emphasizing image analysis (identifying immunoreactive signal in an immunohistochemical stain, making neuroanatomical distinctions in a cytoarchitectural stain) and translation of image data to the brain atlas. Using a quasiexperimental mixed methods approach, we evaluated aspects of student engagement and perceived gains in student confidence with respect to the nature and process of science and student science identity development. Additionally, we examined the dynamics of mentorship and student connectedness experienced in the online-only context. We found that the majority of students reported positive affective outcomes for the course in domains such as project ownership and project engagement in addition to positive responses toward perceived mentorship received during the course. Unsurprisingly, students expressed frustration in not being able to freely communicate with members of the course in an organic face-to-face environment. Furthermore, we found that students encountered greater difficulty in mastering image software skills causing a delay in producing consistent-quality data maps. From our analysis of the course, we have identified both useful approaches and areas for course improvement in any future iterations of the online research course. New & Noteworthy: Herein, we describe the process of converting a novel, face-to-face neuroanatomy course-based undergraduate research experience (CURE) to an online-only research setting. We document student affective and skill gains resultant from participating in this course and examine best practices for structuring online CUREs to maximize student learning and success.