Effective dissemination of information to the public is critical in managing anxiety associated with pandemics and vaccination programs. It implies that healthcare professionals, particularly pharmacists, are primarily responsible for providing precise and reliable information to reduce anxiety. This study aimed to quantify the prevalence of anxiety associated with the COVID-19 vaccine in Indonesia and to test the efficacy of a mobile phone app-based educational intervention in alleviating this specific type of distress. The study used a pre-experimental research design using a one-group pre-test–post-test structure to collect and analyze data. The study was conducted in the Special Region of Yogyakarta, Indonesia, from March to August 2021. According to a descriptive analysis of the pre-intervention data, most participants (n = 268; 56.90%) reported “mild to moderate” concern over the COVID-19 vaccine. However, post-intervention data revealed a significant drop in anxiety levels. Only 36.30% (n = 171) of participants reported “mild to moderate” anxiety, while 27.39% (n = 129) reported “moderate to severe” anxiety. The statistical study, carried out using the Wilcoxon method of hypothesis testing, produced a significant result with a p-value of 0.001, which was much below the usually recognized significance criterion of 0.050. These findings concluded that a mobile phone app-assisted patient education intervention can effectively reduce the HARS questionnaire’s scores among Indonesians. As a recommendation, this study advocates for incorporating a mobile phone app as part of the complete educational infrastructure, since it can serve as an important aid in reducing anxiety associated with COVID-19 vaccines.