The baby, conceived through artificial insemination using donor sperm and Beatie's own eggs, was born on June 29 and Beatie and the baby are "healthy and doing well," it was reported.
He said that contrary to published reports, the baby was not delivered by caesarean section, but no other details about the birth were given.
The thinly bearded Beatie told The Oprah Winfrey Show in April that he began his sexual transformation about 10 years ago when he started testosterone treatment and had surgery to remove mammary glands and flatten his chest.
Upon deciding to have a child about two years ago, he halted his bi-monthly hormone injections and resumed menstruating.
Beatie's wife, Nancy (46), whom he married five years ago, was unable to conceive because of a prior hysterectomy. Otherwise, he said, "I wouldn't be doing this."
Thomas went into labour earlier than expected and was rushed to hospital. He and wife Nancy were seen leaving the St Charles Medical Centre in Bend, Oregon, last night with their new arrival.
The delivery took place amid tight security in a special section of the hospital away from all the other mothers giving birth.
Any callers to the secretive hospital were told that there was no Thomas or Nancy Beatie staying there.
A source at the hospital said: "Thomas gave birth without any problems at all, but amid tight security.
"The baby girl is healthy and mother -- or father -- and baby have been allowed to leave the hospital."
Thomas and Nancy left the hospital by a private exit with a maternity nurse close behind with their new arrival.
They were then escorted away by a team of female security guards.
He now plans to seal a €630,000 deal for pictures of his new baby. As well as this, he has had a documentary film crew following him for the last few months documenting his experiences.
Thomas was born Tracy Lagondino and lived in Hawaii. He had a sex change after falling in love with Nancy, because Hawaiian law bars same-sex marriages.
Thomas previously stated: "We're deeply in love. I'm stable and confident being the man I am. Having this baby doesn't make me less of a man."