YOGYAKARTA, Indonesia — As the call to prayer boomed over this midsize university town on a recent Sunday evening, rows of conservatively dressed Muslim women laid out their prayer mats, bowed toward Mecca and murmured prayers in Arabic. As dusk fell, it was a ritual being carried out in mosques and prayer academies across the city.
What set this academy apart is that most of the worshipers here had been born as men.
Tucked away behind a large mosque on a side street in Yogyakarta, Al Fatah Pesantren is, according to its leader, the only Muslim academy or madrasa for transgender people in the world.
Shinta Ratri, the school’s 53-year-old director, founded it with other transgender women in 2008, two years after a major earthquake convulsed the city. “It was a time of suffering, and transgender people needed a way to pray,” she said. “We needed a place to worship together and learn about Islam.”
Transgender women have few opportunities to worship, as their defiance of strict gender categorization challenges conservative Muslim views about gender.
Yuni Shara, 48, a former office worker who serves as Al Fatah’s secretary, said she found an acceptance here that she did not at local mosques. “People would stare at me at mosque,” she said. “They would point and say, ‘She’s transgender.’ ”
She said it was hard to focus on prayers when people gawked or stared, or when other worshipers would refuse to sit with her.
Sitting on the school’s front porch before a prayer ceremony, she used a hand mirror and tweezers to pluck hair from her chin. “Here,” she said, “it’s very comfortable.”
In Indonesia, transgender women are known as waria, a portmanteau of the Indonesian words for man and woman. Though waria have long been part of Javanese culture, they are shut out of most formal work opportunities and live at the margins of society.
They can become hairdressers at salons, dancers in risqué shows, occasionally even pop stars. Many, though, work the streets, begging during the day and engaging in prostitution or other sex work at night.
“I’ve always been devout,” said Edo, a 39-year-old sex worker who uses only one name, as she sat on the school’s front steps, adjusting her green hijab, which she wore with a conservative black gown. After going out on Saturday evenings to meet clients, she will often head to the school for Sunday worship.
“There’s no contradiction,” she said, crediting this realization to her study at the pesantren, the Indonesian word for madrasa. Like other women here, she goes by a name she chose for herself after transitioning genders.
Such a student body has its challenges. Transgender women often live in poverty with unstable family lives.
The school’s 40 or so students tend to be older than those at a traditional madrasa, who are usually in their teens or early 20s. Some are as young as their late teens, but mostly they are middle-aged and have missed traditional Islamic education because they were expelled from home as teenagers.
“Many students come and go,” Ms. Shinta said.
She wants to bring waria from the edges into the center of Indonesian life. And in this increasingly religious country, that means bringing them into the center of Islam.
While the primary goal of the academy is to provide a place of worship for transgender women, she said, another goal is using Islam to advocate transgender rights. “We have to educate the public about who transgender women are, and we have to push the government so that it acknowledges that we have equal rights,” she said.
Though some transgender Indonesians have succeeded in getting the state to recognize them, Indonesian law offers no protection against workplace discrimination or harassment. Many waria report having been dismissed from their jobs when they expressed their true gender identity, compelling them to select work outside the formal sector, like prostitution, instead.
The school’s students meet during the week to plan trips to local universities, where they speak about Al Fatah’s mission, and to plan religious ceremonies. To raise money for Arabic lessons, Ms. Shinta and many of the students study traditional Javanese dance, which they perform at weddings and other ceremonies.
Their efforts have been championed by progressive Muslim leaders, who embrace the school as a symbol of tolerance at a time when there is widespread worry that Indonesia’s historically tolerant Islamic tradition is being eroded by more doctrinaire forms of Islam imported from the Middle East.
“The pesantren is important for persuading Indonesians that transgender women, as well as L.G.B.T. more generally, are not necessarily sinners or deviants,” said Musdah Mulia, a prominent feminist theologian and chairwoman of the Indonesian Conference on Religion and Peace, an organization that promotes religious tolerance.
Such open support, however, comes exclusively from Indonesian Islam’s most progressive voices. Conservative Muslims, including Indonesia’s Ulama Council, which advises the national government on religious issues, do not acknowledge transgender rights.
Ms. Shinta had hoped that the faculty of Sunan Kalijaga State Islamic University in Yogyakarta would work with her school to develop guidelines for leading a proper Islamic life for transgender people, but the partnership foundered on theological differences.
“In the Quran there are only men and women,” said Fuad Zein, a professor in contemporary Islamic law at the university.
Still, the country’s largest Muslim organization, Nahdlatul Ulama, or N.U., has been “extremely supportive” of the school, Ms. Shinta said.
N.U., which has an estimated 50 million members across Java, follows traditional Javanese Islam, with its generally relaxed interpretations of Islamic law and emphasis on tolerance.
Institutions affiliated with the organization have provided the school with Muslim teachers and connected Ms. Shinta with sympathetic religious leaders and faculty members throughout Java, the island where more than half of Indonesia’s people live.
The irony that a transgender prayer academy is supported by Indonesia’s most prominent traditionalist Muslim group is not lost on Ms. Shinta. “It’s because Javanese culture is far more open to gender issues, because Javanese people were already introduced to transgender women well before Islam arrived,” she said.
Jeremy Menchik, an assistant professor in the Pardee School of Global Studies at Boston University and the author of “Islam and Democracy in Indonesia: Tolerance Without Liberalism,” says that Indonesia challenges common assumptions about where tolerance comes from. “The general idea is the more tolerant individuals will be the more urban, educated, liberal and secular,” he said. “What’s interesting about Indonesia is among the organizations I study, N.U., the traditionalist one, the rural one, the conservative one, is the most tolerant.”
Ms. Shinta, who wears a traditional gamis — a gown worn by observant Muslim women — and a head scarf, in many ways embodies that strain of tolerant conservatism.
Asked about the place of transgender people in Islam, she gives a broad smile and pulls out a Quran, pointing out passages that, she says, prove that Muhammad cared about transgender people. “It’s proof! He cares about us!” she exclaimed, tapping her finger on a passage about a man who does not desire women. “That’s transgender, that’s gay!”