Heintze made his Denmark debut on 29 April 1987 in a Euro 1988 qualifying match, a 1–0 win over Finland, and he played all three matches at the final Euro 1988 tournament, though Denmark lost them all. At the final qualification match for the Euro 1992 against Yugoslavia on 1 May 1991, Heintze's then club, PSV, wanted him to stay home to play an important match for PSV, but he decided to travel with the Denmark team. Once at the Denmark camp, Heintze learned that national coach Richard Møller Nielsen did not intend to start with him in the game, and after consulting PSV, who still wanted him to play, Heintze decided to go back to the Netherlands, without the knowledge of Møller Nielsen. Back in Eindhoven, Heintze found out he wasn't eligible for the PSV match since he had been written off to play for Denmark. Heintze would see the PSV game from the sideline, and as a punishment for leaving the national team, he received a one-year ban from the national team by Møller Nielsen. As the ban expired before the Euro 1992, Heintze was once more called up, but an injury kept him from re-entering the team. Thus, he missed Denmark's later victory in Euro 1992, following Yugoslavia's exclusion from the tournament due to the Yugoslav wars. He played a further four matches under Møller Nielsen, before his national team career went on hiatus.