The founder and CEO of the city’s largest and most successful charter school network abruptly retired on Tuesday.

Mike Milkie, 57, started the first Noble Charter School in 1999 and grew it into a network of 17 campuses, serving more than 12,000 students.

His departure was announced soon after a meeting of Noble’s board of directors. In a letter addressed to the “Noble family,” Board President Allan Muchin said Milkie was ending his tenure “for personal reasons.” Muchin then added, “Given the circumstances involved in his decision, we think this is best for Noble as well. The board intends to further review this situation.”

People at that board meeting say Milkie was visibly upset afterward.

Muchin’s office directed calls to the charter school’s spokesperson, who declined to elaborate.

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Reached later in the day, Milkie reiterated that he was retiring for personal reasons and declined to comment further.

Milkie founded the first Noble campus after working as a teacher at a nearby neighborhood high school. He was frustrated by what he saw as an unruly environment, with too many layers of bureaucracy, some of which he blamed on the teachers union.

He set out to create a highly disciplined environment that was conducive to student learning. If a school “sweated the small stuff,” he thought, bigger problems could be prevented.

But over the years, the code of conduct at the Noble Network of Charter Schools came under increased scrutiny, including a policy of fining students for misconduct. Recently, teachers have been trying to organize a union of their own, but have yet to be successful.

On Tuesday, a group of students presented the board with a petition of 6,000 signatures, demanding that discipline policies be changed. It was unclear whether the petition drive was related to Milkie’s departure.

The students targeted three specific policies, including one that they say limits free speech and a bathroom policy they say is draconian and disrespectful.

Student Xochilt Rivera told board members that a policy requiring students to be escorted to the bathroom can lead to student embarrassment. She said she recently had to ask a teacher twice to call someone to walk her to the bathroom.

She was on her period.

“People started whispering, and they told me that I was stained and I walked out of the classroom and I went to the bathroom and I had a lot of blood and I came back and I got my stuff,” Xochilt said. Staff, she said, told her she could tie her sweatshirt around her waist for the rest of the day.

Similar situations have been reported, but board members seemed shocked, the students said. They also reported that Milkie tried to deny a bathroom escort policy and became defensive when parents at the board meeting confirmed it existed.

Another complaint from students is when teachers forbid students from wearing buttons or talking about political subjects the teachers don’t want discussed. Juan de la Torre said he wants to wear an orange ribbon against gun violence, but has been told he can’t.

“I like the academics. I feel like I am being prepared for college,” Juan said. “But when there is no room for me to grow as a human and discover myself, I don’t like that. In school, I am silenced.”

Diego Garcia said it was his idea to gather petitions to fight the discipline policies. He said students from all of Noble’s 17 campuses signed it.

“I want to quote one of the staff members at my school, ‘we are not just crazy uneducated people just screaming in the streets because clearly we get things accomplished when we get together,’” he said.

But Garcia said he did not believe the petitions alone drove Milkie’s departure. He said he thinks it resulted from steady drumbeat of pressure put on Noble from parents and teachers, as well as current and former students.

Milkie’s retirement is effective the end of the year.

Sarah Karp covers education for WBEZ. Follow her on Twitter at @WBEZeducation and @sskedreporter.