In 2016, the Philippine Department of Health (DOH) introduced a novel dengue vaccine in a mass immunization program to reduce the substantial economic and social burden of the disease on households and the government. The vaccine manufacturer’s announcement regarding new findings on the small but increased risk of severe dengue for vaccinated seronegative patients caused turmoil as various people claimed that the vaccine caused deaths and that health authorities are corrupt. While health department staff split—some having to preserve its reputation and others to monitor over 800,000 children administered the vaccine—communication between the frontline health workers and parents suffered. As a result, public confidence in vaccines dramatically dropped and the repercussions challenge the public health system. We examine factors that contributed to the crisis and argue for strengthening risk communication strategies and increasing transparency on decision making to counter misinformation and protect public health.