According to the American Heritage Dictionary of Idioms, the idiom comes from an older Latin phrase:

"This term came from a Latin proverb, translated as 'Children [boys] are children [boys] and do childish things.' In English it was first recorded in 1589."

Unfortunately, the American Heritage Dictionary doesn't cite the 1589 source.

The Routledge Dictionary of Latin Quotations confirms that this is a Latin phrase:

"sunt pueri pueri, pueri puerilia tractant: children are children, and children occupy themselves with childish things (also, boys are boys, ...)"

Routledge gives the name of a known Latin author when known, but in this case, it does not cite a known author.

The older Cassell's Book of Quotations, Proverbs and Household Words translates it slightly differently:

"Sunt pueri pueri, pueri puerilia tractant.— Boys are boys, and boys employ themselves with boyish matters."

That resource also doesn't give a singular Latin source for it, just citing it as a proverb.

The Oxford English Dictionary cites the specific English language phrase of "boys will be boys" as first appearing in a 1770 letter collected in A Series of Genuine Letters Between Henry and Frances by Richard Griffith and Elizabeth Griffith (a married couple - the collection is a series of letters they exchanged through their courtship and marriage). It's found in Vol VI, in letter DCCXVIII:

"Heaven bless them both!—though Jack is under a Cloud with me at present—but Boys will be Boys—and I endeavour to make my philosophy like yours—severe only to itself."

If the American Heritage Dictionary of Idioms is correct with its 1589 date, it's likely that variations on the phrase were in use much earlier than 1770. And considering that it comes from Latin, it's quite possible the phrase was adopted from Roman Britain into pre-English British languages and was known right from the start of the Old English language in the ~4th Century CE, though that's only speculation. It could also have come later through the Catholic church or something.

Has it ever worked for girls?

Yes. The Oxford English Dictionary documents the phrase "girls will be girls" as having been in use at least as early as 1826 in the English language. Thomas Henry Lister used it that year in his book Granby: A Novel, published in London:

‘She really used him rather ill.’

‘How so?’

..

‘Why, girls will be girls. They like admiration.’

The OED gives other citations for this variation in 1873, 1953, and 2006, showing that it is still in use, if relatively uncommon.

One last item: while none of the resources mention it, there's a well-known proverbial phrase found in the Bible verse 1 Corinthians 13:11:

"When I was a child, I spoke as a child, I understood as a child, I thought as a child; but when I became a man, I put away childish things."

There might be some connection there to the Latin proverb, though since no source mentions it, I would assume that etymologists aren't willing to necessarily jump to that conclusion. Classical Latin was being spoken at the time Corinthians is thought to have been written, in the 1st Century CE, so if there is a connection, the Bible's use of it may be borrowing it from the Latin, and not the other way around. Then again, from what I understand (and I'm no Bible scholar by any means, so take it for what it's worth), Corinthians was originally written in Koine Greek, so there's a possibility that some variation on "boys will be boys" or "children act like children and do childish things" was known in Ancient Greece before it was being used in Rome, but the earliest preserved uses of it come from Latin documents later on.