The ordinance would have prohibited discrimination of LGBT residents in the areas of employment, housing and public accommodations.
The vote Tuesday was 3-2 and a second reading must be approved before the ordinance is officially repealed, the Associated Press reported.
The previous commission had passed the ordinance in February, making Manhattan the second city in the state to protect people from discrimination based on sexual orientation. But new council members were elected in April and opponents of the ordinance continued to push for its repeal.
Commissioner Wynn Butler said he supported the repeal because the amended ordinance puts Manhattan city law in front of Kansas law.