Jacquelynn Vance-Pauls, a real-estate lawyer in upstate New York, has a 14-year-old son with autism who was recently kicked out of his private special needs school. Her 9-year-old twins and her high-school senior are also on the verge of being expelled from their public schools.

The children did not do anything wrong, nor are they sick. Instead, Ms. Vance-Pauls has resisted complying with a new state law, enacted amid a measles outbreak, that ended religious exemptions to vaccinations for children in all schools and child care centers.

Ms. Vance-Pauls said she believed vaccines contributed to her son’s autism, despite more than a dozen peer-reviewed studies showing no such link. The Bible, she said, barred her as a Christian from “desecrating the body,” which is what she says vaccines do.

“If you have a child who you gave peanut butter to and he almost died, why would you give it to your next child?” she said during an interview in August, trying to explain her fears. “How do we turn our backs against what we have believed all these years because we have a gun to our heads?”

With the start of school this week, Ms. Vance-Pauls, along with the parents of about 26,000 other New York children who previously had obtained religious exemptions to vaccinations, are facing a moment of reckoning.

Under the new law, all children must begin getting their vaccines within the first two weeks of classes and complete them by the end of the school year. Otherwise, their parents must home school them or move out of the state.

The measles outbreak that prompted the new law is actually easing. On Tuesday, Mayor Bill de Blasio declared an end to the measles outbreak in New York City, its epicenter. Since the start of the outbreak in October 2018, there have been 654 measles cases in the city and 414 in other parts of the state, where transmission has also slowed.

The large majority of cases have involved unvaccinated children in Hasidic Jewish communities, where immunization rates were sometimes far lower than the state average of 96 percent. Wide-scale vaccination campaigns have helped lift those rates.

But health officials warned on Tuesday that as school begins the highly contagious disease could easily return, particularly if vaccination rates drop again.

“The threat remains, given other outbreaks in the U.S. and around the world,” said Dr. Oxiris Barbot, the city’s health commissioner. “Our best defense against renewed transmission is having a well-immunized city.”

With the passage of the new law on June 13, New York became only the fifth state to bar all nonmedical exemptions to vaccination and now has among the strictest policies in the nation.

Maine, where a new law barring all but medical exemptions does not go into effect until 2021, makes exceptions for special education students. California, where nonmedical exemptions were ended in 2015, gave parents with nonmedical exemptions extra time to comply, and allowed districts to exempt disabled children.

The New York law allows no such exceptions.

The anti-vaccination community in New York has filed several lawsuits seeking to block the legislation, but none have succeeded so far.

At the same time, state health officials have been moving to close additional loopholes, announcing in August emergency regulations that make medical exemptions to vaccination harder to get. (In California, officials said, the medical exemption rate to vaccination increased from 0.2 percent to nearly 1 percent after other exemptions were eliminated, dulling the law’s intended impact.)

“I assure you, vaccines are safe and effective,” Dr. Howard A. Zucker, the state health commissioner, says in a public service announcement running on television. “I’m a father,” he adds. “My kids are vaccinated.”

The law is already encouraging parents on the fence about vaccination to immunize their children, and is sending a message to public and private schools that the days of selective vaccination are over. But for parents who remain deeply skeptical, more steps will be needed, according to doctors who study vaccine refusal.

Dr. Daniel Salmon, the director of the Institute for Vaccine Safety at the Johns Hopkins Bloomberg School of Public Health, pointed out that unease about vaccines is not just a fringe issue. A 2011 study, for example, found that roughly a quarter of all American parents had serious concerns about vaccines and 30 percent worried that vaccines may cause learning disabilities, such as autism.

Eliminating nonmedical exemptions is a partial solution, Dr. Salmon said, adding that more research funding was needed to study the safety of vaccines and to counteract the anti-vaccine lobby.

“It’s a big hammer that isn’t getting at the big problem,” he said. “Parents have concerns that aren’t being addressed.”

Lorna R. Lewis, the superintendent of the Plainview-Old Bethpage Central School District in Long Island, helped lobby for the law as president of a state superintendents council. She estimated that of the 65 children who had religious exemptions in her district, about 10 would likely be home schooled.

“We have 5,000 students in my district,” she said. “If there are 10 that have hard-standing vaccine adverse parents, I have 4,990 others who I have to think about.”

Parents have already asked that their children not be placed in classes with unvaccinated children, Ms. Lewis said. “I think in a society you have to do what’s best for the good of all,” she added, “and I think that’s what this law does.”

In the state’s Mennonite and Amish communities, where some schools had high religious exemption rates, health officials reported progress following meetings about the vaccination requirements.

In Yates County in the Finger Lakes region, “well over 50 children” scheduled appointments to get their shots in late August, said Deborah Minor, director of public health for Yates and Schuyler Counties.

“My sense is that the schools are taking this very seriously,” she said.

Rabbi Yakov Horowitz, the founding dean of Yeshiva Darchei Noam in Rockland County, said public sentiment in his Orthodox Jewish community had “shifted significantly” toward vaccination over the past year because of the measles outbreak, public health outreach and supportive statements by influential rabbis.

“Hopefully, most people will abide,” said Dr. Patricia Schnabel Ruppert, the health commissioner of Rockland County. But she also said that because her efforts had been focused only on preventing measles, there was much more education to do about vaccines to protect against other diseases.

Some parents who do not want to vaccinate their children are turning to home schooling to avoid running afoul of the new mandates. Under state law, home-schooled children may meet in cooperative learning groups for up to three hours a day.

Miss Megan, a home schooling consultant, said she was opening a new home-school cooperative in the Chelsea neighborhood of Manhattan for parents who do not want to comply with the new order. Some, she said, were forfeiting hefty deposits at private schools. Some, she added, were not against vaccination, but wanted to space out the timing of the shots more than the law will allow.

“It’s a very overwhelming position that a lot of the kids are being put in,” she said.

Kristina Staykova, 43, said she was shutting down her fashion business as she tries to figure out how to home school her children, including a 4-year-old with autism. Her 5-year-old daughter has already been told not to return to Public School 6 on Manhattan’s Upper East Side.

She recently went to a home-schooling conference in Melville, N.Y., where there were about 300 parents, most of whom, like her, believed that their children had been injured by vaccines, she said.

Part of the challenge facing health officials across the country, said Peter Hotez, dean of the National School of Tropical Medicine at the Baylor College of Medicine in Texas, is that steps should have been taken years ago to reduce nonmedical exemptions before they became more common and anti-vaccine activism spread.

Still, only a tiny fraction of New York children had religious exemptions: about 0.8 percent of all school children statewide in 2017-18, the last school year for which data was available.

The problem was that unvaccinated children tended to be clustered in communities, driving down vaccination rates in certain schools and neighborhoods to under 95 percent and creating potential tinder boxes for outbreaks, Dr. Hotez said.

Some schools that operate throughout the state and have low vaccination rates, such as Waldorf schools, are now figuring out how to handle shifts in enrollment as some of their families turn to home schooling. Even in some public districts, administrators have called for more time to ensure that children being pulled from school by their parents do not suffer educationally.

For Ms. Vance-Pauls, Tuesday marked the end of the line. With school starting on Wednesday, she had made a 6:30 p.m. appointment with a doctor on Tuesday for each of her children to get one shot apiece, and appointments over the coming weeks for the rest of the required shots.

Her family did not have the option to home school or move so she felt she had no other choice.

“I’m praying to God that my twins are now 9 and can handle what Jack couldn’t handle when he was a baby,” Ms. Vance-Pauls said, referring to her autistic son. “I feel like there is nowhere for us to run.”

Sharon Otterman has been a reporter at The Times since 2008, primarily covering education and religion for Metro. She won a Polk Award for Justice Reporting in 2013 for her role in exposing a pattern of wrongful convictions in Brooklyn. @sharonNYT

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