Flu vaccination coverage rates have been concerningly low on college campuses, but it is unclear what college students know about the vaccine or how their knowledge relates to their intrinsic motivation and vaccination intentions. To inform vaccine-related teaching, I explored students’ knowledge using the Actional perspective of knowledge construction, which suggests that erroneous conceptions are deviations from or precursors of accurate knowledge; I examined students’ intrinsic motivation using the 3 components of Self-Determination Theory (Autonomy, Competence, and Relatedness); and I measured a spectrum of students’ vaccination intentions. From an urban public university, we recruited 369 students from three levels of biology courses and 25 immunology faculty as expert controls. We used Likert-type questions to capture students’ flu-vaccine-related intrinsic motivation and vaccination intentions. I assessed knowledge about how the flu vaccine works with three open-ended questions, and responses were analyzed with a rubric to quantify basic knowledge and alternative conceptions. I used logistic regression modeling to identify correlations between knowledge and vaccination intentions. Unfortunately, factor analysis revealed that my study cannot distinguish the 3 components of intrinsic motivation. I found that the presence of certain alternative conceptions is correlated with the absence of basic knowledge about how the flu vaccine works. Additionally, knowing about the vaccine’s preventative power is related to intention to vaccinate, yet believing in the flu-causing effects of vaccination is related to intention to not vaccinate. My findings highlight common gaps in college students’ vaccine-related knowledge and contribute to current understanding of how knowledge relates to vaccination intention.