Sources close to the couple say that it was a "natural childbirth" and that they have not yet decided on the boy's name. Beatie's wife, Nancy, will be breastfeeding their son, as she did with their daughter, Susan Juliette, who was born last June.
Photos of a bearded Beatie with a pregnant belly caused a sensation last year, leading to headlines about the world's first "pregnant man."
Born a woman named Tracy, Thomas Beatie, now 35, had sex-reassignment surgery and legally changed his gender from female to male in Hawaii.
Beatie, who kept his female reproductive organs, says that he decided to bear children, when his wife Nancy, 46, was not able to.
The couple described their unusual path to parenthood in an exclusive interview with Barbara Walters last year, during which they revealed that Thomas was expecting a second child.
Then in his first trimester, Beatie told Walters he did not go back on the male hormone testosterone after Susan's birth so he could have another baby.
"I feel good," he said. "I had my checkups with my hormone level, as far as the HCG. And everything is right on track."
In last year's exclusive interview, Beatie spoke to Walters about Susan's birth, which was also not via Caesarean section. He was in labor for 40 hours; Nancy Beatie cut the umbilical cord.
Last spring, Thomas Beatie wrote an article in the national gay magazine The Advocate, revealing that he was legally male and that he was pregnant. He released a photo showing his bearded face and pregnant belly. The news -- and the controversial photo -- ignited a media frenzy and provoked questions about traditional notions about sex and gender.
"Hiding a pregnant man is like hiding an 800-pound gorilla," he said of his decision to go public. "Nancy and I wanted to tell our story from our own mouths before it got out."
Beatie says he was surprised at how quickly the news of the "pregnant man" spread.
"I was shocked that it looped around the world in 24 hours," he told Walters. "I mean, it was on Chinese Web sites and, you know, Web sites in Romania and Russia and Brazil."
He became an instant target of the tabloids and paparazzi, and fodder for talk shows and late-night television. Some people called Beatie a freak. He received death threats, and thousands of hateful comments still litter the Internet. To this day, he continues to receive anonymous hate messages.
For months after Susan's birth, Thomas Beatie, 35, and his wife, Nancy Beatie, 46, lived a quiet life in Bend, Ore., where they own a tee shirt company called Define Normal.
Despite concerns for his family's safety, Thomas Beatie said he won't let fear rule their lives and he feels they are a traditional family.
"We are a man, woman and child. It's ironic that we are so different but yet, we're just a family, just the same as anyone else," he said.
When asked why he makes many people uneasy, Beatie said, "I think that people are not used to seeing the image of a pregnant man. And it's causing a lot of people to think. … I used my female reproductive organs to become a father."
Thomas Beatie was born Tracy and grew up in Hawaii. A beautiful young girl, Beatie said he never felt particularly feminine growing up.