The decision came on Friday as HISD reorganizes amid a state takeover.
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All affected custodians have been notified of the position's discontinuation, and "they are free to reapply for other open positions in the district," HISD said in a statement to the Chronicle.
"This is part of our ongoing effort to right-size the central office to ensure we are using resources responsibly and maximize resources in the classroom," the statement said.
The statement said the HISD followed the guidelines of human resources when managing the layoffs.
Mayor Sylvester Turner posted on X, formerly known as Twitter, questioning when enough is enough.
"How much more will we accept by those currently in charge of HISD put there by the state before we collectively stand up and say enough," Turner said.
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The number of jobs cut hasn't been released.
Michelle Williams, president of the Houston Education Association, told the Houston Chronicle that safety concerns could arise from the layoffs since custodians secure school buildings in the morning and lock up when the day is over.
HISD has continued to make cuts, including more than 2,300 administrative jobs, after the Texas Education Agency took over the district earlier this year.
The sudden announcement has a familiar tone. In August, the district used prerecorded video announcing 21 special education teachers' job cuts, which also came as a shock.