According to the World Health Organization (WHO), vaccination has significantly reduced the burden of infectious diseases. However, low disease rates do not eliminate the need for continuous monitoring to address the threat of potential outbreaks. The presence of unimmunized individuals can place any community at risk of disease outbreaks. This review aimed to explore the ethical challenges associated with parental refusal to vaccinate children and to identify knowledge gaps in this area for further research within the country. A comprehensive search was conducted using PubMed and ScienceDirect. The final selection included 35 academic articles, one book, and one master’s thesis. In Iran, as in many other countries, anti-vaccination movements have grown in recent years, particularly following the rollout of COVID-19 vaccines. These movements often oppose vaccination for reasons such as philosophical or religious beliefs, poor health literacy, mistrust in healthcare systems, and personal or social experiences. The debate surrounding mandatory vaccination has persisted, primarily due to ethical concerns about coercion. One of the central ethical challenges involves the conflict between parental autonomy and public health. The degree to which parental autonomy is respected is a critical issue in the ethics of vaccination. Factors such as misinformation, inadequate information, or misinterpretation of information can constrain parental autonomy. Conversely, the state has a duty and vested interest in safeguarding children from harm, which may lead to challenging parental autonomy in cases where a child’s well-being is at risk. In conclusion, the extent of parental autonomy in planned interventions such as vaccination depends on the balance between the benefits and burdens of the intervention, taking into account the ethical principles of beneficence and non-maleficence. The greater the benefit, the less decisive parental autonomy becomes, and vice versa. Various studies addressing this issue have proposed strategies such as public education, organizing community-level vaccination discussions, educating vaccine-hesitant parents with evidence-based information, providing trustworthy resources for research, identifying factors influencing parental autonomy, conducting regular follow-ups, and implementing negative policies, including legal enforcement, fines, and restrictions on access to daycare centers and schools.