This death left the king's younger brother, Prince Philippe, Count of Flanders, as the only person in line for the Belgian throne.

[1] Baudouin died of influenza in the Palace of the Count of Flanders on 23 January 1891, a day after the anniversary of his cousin Leopold's death from pneumonia.

Rumours circulated after his death that foul play had been involved, including a suggestion that Baudouin's death was a copy of the suicide of Crown Prince Rudolf of Austria; Rudolf was the husband of Baudouin's cousin, Stéphanie.

[2] Upon the death, the Belgian Parliament was adjourned and theatres and public institutions were closed until after the funeral.

Baudouin's body was interred at the royal vault at the Church of Our Lady of Laeken in Brussels.