This longitudinal study investigates executive functions (EF) in children with transposition of the great arteries (TGA) compared to typically developing children at a key age period between 5 and 7 years. We explored the presence and evolution of specific impairments on three core EF components (inhibition, working memory, and cognitive flexibility). Ninety children were evaluated for three consecutive years. Results demonstrated significant delays in inhibition and cognitive flexibility despite normal working memory. Impairments did not systematically worsen with age. EF impairments after TGA are dynamic and may affect selective components. Cyanotic congenital heart disease is associated with altered EF development.