Congenital syphilis (CS) is a major cause of mortality in several countries, especially in Latin America and the Caribbean. This study aimed to analyze fetal and infant mortality of CS reported to the Health Information System in a State in Northeastern Brazil. This was a cross-sectional study that analyzed the deaths of CS from 2010 to 2014 through the linkage of the Mortality Information System (SIM) and the Notifiable Diseases Information System (Sinan). The Statistical Package for the Social Sciences (SPSS) version 23.0 was used to calculate the rates of Fetal, Perinatal, Neonatal (early and late), and Postneonatal Mortality. Simple linear regression was performed. Fisher's exact test or Pearson's chi-square test were used for comparison of proportions and Student's t-test was used for comparison of means. Of the 414 cases reported to the SIM as deaths possibly caused by CS, 44 (10.6%) presented CS as the underlying cause. From 2010 to 2014 the Infant Mortality Rate of CS was 16.3 per 100,000 live births (y = 0.65x + 14.33, R2 = 0.2338, p = 0.003). There was an 89.4% underreporting of deaths. Perinatal deaths and fetal deaths of CS accounted for 87.7% and 73.9% of total deaths, respectively. The results of the study revealed a significant Fetal and Infant Mortality rate of CS and demonstrated the importance of using the linkage method in studies that involve the analysis of secondary data obtained from mortality and disease reporting systems. The underreporting of CS as a cause of fetal and infant mortality leads to unawareness of the reality of deaths from this disease, hindering the development of public policies aimed at its prevention.