The free courses increased scores an average of 115 points from earlier and preliminary scores.
Sal Khan says the new arrangements are the first he has forged with large, diverse school districts.
Officials said free test prep will "level the playing field" for all students.
Over the past decade, the free instructional website Khan Academy has transformed how tens of millions of students across the globe perceive and approach math. Now, it’s pursuing a bigger aim: transforming how students perceive themselves.