Madagascar made its Paralympic Games début at the 2000 Summer Paralympics in Sydney. Its sole representative, Aina Onja, was a blind sprinter who ran the men's 100m sprint in the T11 category. His time of 13.98 was the slowest in the heats, and he did not advance to the semi-finals.
The country was absent from the 2004 Games, but returned to the Paralympics in 2008, represented by a single male swimmer. Josefa Harijaona Randrianony swam in the 50m freestyle (S9 category), and finished last of his heat in 38.06s.
Madagascar has never competed at the Winter Paralympics.