His remarks came a day after education secretary Betsy DeVos was criticised for defending a proposed $17.6m (£13.5m) cut to the organisation, which is designed for disabled children.
The request was included in Mr Trump's $4.75tn federal budget, which was not expected to pass Congress.
Mrs DeVos responded she had pushed for funding "behind the scenes".
"I heard about it this morning. I have overridden my people. We're funding the Special Olympics," Mr Trump said of the world's largest sport organisation for people with intellectual disabilities.
Mrs DeVos rushed to clarify the contradiction on Thursday, tweeting: "I am pleased and grateful the President and I see eye-to-eye on this issue and that he has decided to fund our Special Olympics grant."
She had earlier told Congress the US Department of Education had to make "tough choices" following a 10% cut to her agency's budget, adding that the nonprofit group should be funded through private donations.