BACKGROUND To determine the magnitude and temporal trends of deaths due to congenital heart disease (CHD) in Pernambuco between 1996 and 2016. METHODS This was an ecological, time-series study, involving all cases of deaths from congenital cardiovascular malformations in the state of Pernambuco, from 1996 to 2016, using data from DATASUS, SINASC and SIM. RESULTS There were 3,584 deaths from congenital cardiovascular malformations amongst individuals aged 0 to 14 years, of which 81.94% were concentrated in children aged under one year. The infant mortality rate (IMR) presented a linear growth trend of 0.4645 per year (p <0.01). The cause-of-death code Q24 (other congenital malformations of the heart) was present in 72.54% of the death records and 48.17% of the deaths occurred in infants aged between 28 and 364 days of life. The highest occurrence of deaths was identified in children with low birth weight (500 and 1,499g), male, premature, children of mothers without schooling, in deliveries at home (p <0.05). CONCLUSIONS Congenital heart disease still represents a public health problem as a cause of death, particularly in the first year of life, with IMR in a linear growth trend. Deaths from CHD were more prevalent in male children, born prematurely, with low birth weight, born to mothers with low schooling and deliveries without medical care.