Obama will instead speak at a "Senior Recognition Day" for the district, Topeka Unified School District 501, on May 16, the day before graduation.
A petition on Change.org, which had nearly 2,800 signatures at the time of the White House's decision, said students had been thrilled their district had been able to get the first lady for commencement, but that the logistics would make the day a nightmare.
Students would have been limited to no more than six tickets for guests to attend the graduation ceremony, held at the Kansas Expocenter. A spokesman for USD 501 said an estimated 7,800 seats would have been available for the graduates of the five high schools and their guests and the combined ceremony.
The petition estimated that, between the combined ceremony and additional security measures, commencement day could stretch to eight hours.
A statement from the first lady's office said they had been "eager to find a solution that enabled all of the students and families to celebrate the special day."
Obama's speech will also commemorate the 60th anniversary of the landmark Brown v. Board of Education Supreme Court case that desegregated public schools.
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