Appalachia has low rates of college attendance and graduation, but relevant data investigating student attrition from physiology majors in this region are lacking. This exploratory study examined freshman attrition from an undergraduate exercise physiology program in Appalachia with the goal of identifying potential strategies for improving retention across similar programs in this underserved region. Questionnaires were administered at the beginning and end of the fall semester to freshman (n = 247) and students transferring out of the major [Transferred group (T); n = 50] by the end of their first semester were compared against those that remained [Retained group (R); n = 190]. The Transferred group was invited to participate in qualitative interviews. Fewer Transferred students reported feeling underprepared in academic preparedness skills, but more reported feeling underprepared in math. At the end of the semester, more in the Transferred group reported doing worse than expected in math and in getting good grades and had a lower grade point average (R: 3.27 ± 0.05; T: 2.62 ± 0.15; P < 0.01). More in the Transferred group were first-generation (FG) college students (R: 17%; T: 30%). Transferred FG had lower academic preparation and performance and more financial need than Retained FG. In interviews (n = 35), most students expressed a change in career goals and many noted the academic rigor of the program, while academic advising, faculty, and the major received generally positive praise. This study identified several factors that would allow for early identification of incoming freshmen at risk for attrition and proposes strategies for improving retention within Appalachian physiology programs.