Mortality from congenital heart disease has decreased considerably in the last two decades due to improvements in overall health care. However, there are barriers to access to healthcare in Latin America for this population, which could be related to factors such as healthcare system, policies, resources, geographic, cultural, educational, and psychological factors. Understanding the barriers to access to care is of paramount importance for the design and implementation of policies and facilitate the provision of care. The aim of the study was to investigate the perception of barriers to access to health care on parents/guardians of children with congenital heart disease in selected Latin American countries. A descriptive, cross-sectional study, in which parents/guardians or primary caregivers of children with congenital heart disease was recruited to participate and surveyed. Once the informed consent process had been completed, a set of paper-based scales was used to collect data, namely socioeconomic and demographic information, the Barriers to Care for Children with Special Health Care Needs Questionnaire, and the General Health Questionnaire. In total, 286 participants completed the surveys, with an average age of 34.81 years and 73.4% being female. Mean score of overall barriers was 54.45 (minimum score 39, maximum score 195, higher scores show greater perception of barriers). In Mexico, the parents/guardians of children perceived fewer barriers to access (46.69), while Peru is the country where the most barriers were perceived (69.91). Nonpoor participants showed higher overall barrier perception scores (57.34) than poor participants (52.58). The regression analysis demonstrated the overall perception of barriers was positively associated with individual and social factors, such as educational level, contract status, household monthly income, and psychological well-being and with the country of the participants. Multiple factors are associated with the perception of barriers to accessing health care for children with congenital heart disease, including socioeconomic status, expectations, psychological well-being, and structural factors.