To inform the dynamic adjustments of vaccination campaigns, this study examined the transitions among vaccine hesitancy profiles over the COVID-19 pandemic progression and their predictors and outcomes. The transition patterns among hesitancy profiles over three periods were identified using a latent transition analysis with individuals from a longitudinal cohort study since the emergence of COVID-19 in Hong Kong. Four profiles (i.e., skeptics, apathetics, fence-sitters, and believers) emerged consistently over time. From Period 1 (third and fourth pandemic waves) to Period 2 (dormant period, vaccine rollout), 14.17% of believers became fence-sitters (ambivalization), and 12.11% of fence-sitters became apathetics (apathetization). From Period 2 to Period 3 (omicron surge and vaccine mandates), 20.21% of believers became fence-sitters. Lower trust in government predicted a transition to skepticism, whereas higher trust predicted the opposite. Staying as believers was associated with decreased hygienic and social distancing behavior. The stable hesitancy profiles amid the rapid vaccine uptake suggest that structural factors rather than personal agency may drive the surge. Ambivalization and apathetization may signal disengagement in preventive behaviors. Trust in the government is crucial in the pandemic response. Public health interventions may improve compliance with guidelines and prevent skepticism and apathy.