James had said in an interview that Mr Trump was divisive and had emboldened racists.
In response, Mr Trump questioned James' intelligence, saying it was not easy to make the NBA player "look smart".
However, Mrs Trump's spokeswoman said James was "working to do good things" with a school in his Ohio hometown.
She said Mrs Trump wanted "to have an open dialogue about issues facing children".
Earlier this week, James told CNN during an interview with Don Lemon that sport had offered him the opportunity to meet people of different backgrounds and race.