Almost three years after his father came out as transgender, Jonathan Williams found himself standing in a Midtown hotel hallway, hesitating outside his father’s room. As he raised his hand to knock, the surreality of the situation struck him: The person he was meeting was both a beloved family member and a complete stranger.

A curly-haired woman named Paula opened the door.

“She looked nothing like my dad,” Jonathan, a church pastor, tells The Post. “It was almost otherworldly. I tried not to pass out.”

Since learning that his father — also a pastor — identified as a woman in fall 2012, Jonathan, who writes about coping with his father’s transition in the new book “She’s My Dad,” had profoundly struggled with the news.

Growing up in a fundamentalist Christian household, he had been raised with certain beliefs, including that a man who wanted to wear women’s clothes was sick or depraved. Although Jonathan considered himself more progressive than his parents — he scoffed at the church’s dismissal of evolution, for instance — his father’s revelation shook him. He felt betrayed, angry and a profound sense of grief.

“In some ways, it felt like dealing with death,” Jonathan, now 41, says of that time. He had hoped meeting in person might help, but it just made things feel harder. After he met Paula, he shut her out for months.

His reaction was exactly what Paula had been “terrified” of.

“All I ever wanted was to be a good father,” the 67-year-old, who contributes her thoughts to the book as well, tells The Post. Although she knew she was female since the age of 3, “I thought I could just fight it, or cure it with marriage,” Paula says. She had a highly successful life as a man, raising a family in Long Island and rising to the top of the Orchard Group, a conservative organization that establishes new evangelical churches around the world.

It wasn’t until she was 61 years old that “the call to authenticity” struck her. She told her wife she was going to start living as a woman and began taking hormones. Their marriage didn’t survive the shift.

Paula lost her job soon, too, and was shunned by her former friends and colleagues. But she says by far the hardest part of her transition was telling her kids.

“I loved being a father. That was the part of being male that always felt comfortable.”

Jonathan and his two sisters wrestled with the news.

“I was depressed,” says Jonathan, a married father of two who founded Brooklyn’s Forefront Church just three months before Paula came out. “I didn’t want to get out of bed in the morning.” He says he drank heavily to get through his social commitments — which, as an upstart pastor, were extensive — and wondered how much of his fundamentalist background he should continue weaving into his work as a religious leader.

But, eventually, a mix of therapy and time helped Jonathan start coming to terms with his father’s new life. Eight months after meeting Paula for the first time, he asked her to come back to New York.

‘In some ways, it felt like dealing with death.’

Paula says that she understands why it took him so long to come around.

“I exploded the family narrative,” she says. She told her son, “You’re allowed to have the feelings you have.”

One sunny morning in May 2016, the pair took a long walk from Jonathan’s apartment in Carroll Gardens and ended up by the waterfront. There, in the shadow of the Brooklyn Bridge, Jonathan was finally honest about the effect Paula’s transition had had on him.

“It wasn’t just, ‘I can’t believe you became a woman,’ ” Jonathan recalls. “It was also like, ‘When I was a teenager you came down really hard on me.’ Pandora’s box opened up.”

Paula opened up, too. “Basically, she was like, . . . ‘Start seeing things from my perspective, as someone who is repressing their identity,’ ” Jonathan remembers.

“That was a real eye-opener to me,” says Jonathan, who apologized that day. “I love my dad, dearly. At the end of the day, estrangement wasn’t an option.”

Weeks after that conversation, he risked the future of his fledgling evangelical church and began openly welcoming people from the LGBTQ community.

“I think seeing Paula go through what she went through makes me feel like this is almost a calling,” he says. He estimates that today, roughly a quarter of Forefront’s 300 members identify as LGBTQ.

Much to her own surprise, Paula returned to the church, too.

“My rejection from that world was rather complete,” she says. So when she found herself compelled back to the pulpit, preaching a new, more inclusive gospel, “It was like, holy s - - t, wow.”

Nine months ago, the divorcée formally started a progressive congregation, called Left Hand Church in Longmont, Colo. It’s fronted by her, as well as two gay pastors (Jonathan is a proud investor).

Although they still have the occasional “tough” moment, Paula says that conversation with Jonathan under the bridge was a turning point for them as parent and son.

“There was a sense of something redemptive and holy going on,” she says. “I knew that the worst of it was over.”