Background: Vaccine hesitancy is a global concern wherein contributing factors are lack of vaccine confidence, mistrust, alternative parental beliefs, and inadequate information. Methods: This study assessed and compared vaccine-related perceptions of pharmacy students and their guardians in the Philippines through a cross-sectional design survey using the 5C scale (confidence, complacency, constraints, calculations, and collective responsibility). Recruitment was stratified to ensure findings are equally represented. Bivariate non-parametric tests and linear regression analyses were applied. Results: Findings revealed that students were more confident towards vaccines (p = 0.035), and more socially responsible (p = 0.023), while parents were more likely to seek vaccine-related information (p = 0.013). Students were less complacent (p = 0.014) to immunity and less likely to be hindered in getting vaccinated. Predictors of good vaccine-related behaviours were determined to affect the perceptions of students and parents. Higher health literacy has a positive impact on perceptions of vaccination. Conclusion: This study identified a significant intergenerational difference in vaccine perception, which prompts vaccine-related information dissemination to be more targeted.