His comments came after Warren pledged to allow an unidentified "young trans person" to veto her pick for leading the Education Department.
"Now, [former President Barack] Obama said people just don't want crazy stuff," Maher said during Friday's "Real Time with Bill Maher."
"Is this not crazy stuff?" he said, while also jokingly asking if Warren was running to serve as "President of Berkeley."
Prior to those comments, Maher was discussing Warren's and Sen. Bernie Sanders' candidacies for the Democratic nomination. Maher said that he's "always liked" Warren, but "she kind of [...] did some stuff I didn't like," he said, before discussing Warren's comments about the Education Secretary.
During a campaign event in Iowa Sunday, Warren laid out her decision.
"A young trans person [had] asked about a welcoming community and I said, 'It starts with the Secretary of Education, who has a lot to do with where we spend our money' ... and I said, 'I'm going to have a Secretary of Education that this young trans person interviews on my behalf,'" Warren said.
She added that "only if this person believes that our Secretary of Education nominee is committed to creating a welcoming environment, a safe environment and a full educational curriculum for everyone, will that person be advanced to actually be Secretary of Education."
It's unclear who exactly Warren was referring to, but a 9-year-old who identifies as transgender previously asked Warren what she would do in her "first week as president to make sure kids like me feel safer in school." The child then asked, “And what do you think schools should do better so that I don’t have to worry about anything but my homework?”
The initial questions came during a CNN town hall when Warren famously ridiculed conservatives who held traditional views on marriage. The answer appeared to be teed up by a donor who led the liberal organization co-hosting the town hall.
Warren's comments seemed to fit a pattern of making bold pledges surrounding gender. Earlier this month, Warren said she would "build a cabinet and senior leadership team that reflects the full diversity of America, including having at least 50 [percent] of cabinet positions filled by women and nonbinary people."