Background/Objectives: Healthcare professionals’ (HCPs’) accurate knowledge of and positive attitudes toward immunization greatly influence society’s acceptance of it. Early and appropriate immunization education for HCP students is vital. This study aimed to understand current immunization education and vaccine hesitancy among medical, nursing, and pharmacy students in Japan. Methods: An anonymous self-administered online questionnaire was administered to final-year medical, nursing, and pharmacy students in Japan between 6 and 31 March 2023. Survey items assessed current immunization education, preparedness for clinical practice, immunization knowledge, and the degree of vaccine hesitancy. Results: Overall, 525 students (127 (24.2%) medical, 252 (48.0%) nursing, and 146 (27.8%) pharmacy) responded, of whom 39.8% raised concerns regarding new vaccine risks (24.4%,15.9%, and 23.3%, respectively; p = 0.22) and adverse effects (14.2%, 12.7%, and 17.1%, respectively; p = 0.57), including trust in government information (61.4%, 50/4%, and 56.8%, respectively; p = 0.337) or recommended vaccines (57.5%, 4.7%, and 43.8%, respectively; p = 0.113). Preparedness for future clinical practice varied significantly among schools, with medical students (54%) feeling more prepared compared to nursing (34.3%) and pharmacy students (39.1%) (p < 0.001). The average correct immunization knowledge rate was 59.9%, with significant differences between schools (medical 62.7%, nursing 57.6%, and pharmacy 59.6%; p < 0.001). There was no significant correlation between knowledge level and self-assessed preparedness (r = 0.066, p = 0.132). The HCP students wished to receive more immunization education and sought improvements in comprehensive knowledge, communication skills, and practice-based content. Conclusions: For Japan’s HCP students, the enhancement of immunization education focusing on hesitancy and risk–benefit communication is necessary.