Since most people imagine God as an bearded old man, the natural antithesis of this expectation would be having the supreme ruler of the universe be a young girl instead. Creators will sometimes do this to subvert a viewer's expectations, especially in works heavy with Epileptic Trees and Mind Screw.
Compare Divine Race Lift, Goo Goo Godlike, Little Miss Badass.
She personally denies it quite vigorously. The implications are that she could be God if she wanted to, but doesn't think that's what the world needs. There also may or may not be something above her better deserving of the title, but he isn't exactly a conventional deity either, assuming that he's not just her creation, as well. Mind Screw, ahoy!
The premise of Kamichu!!. The full title actually means "The Goddess, A Middle-School Girl"
Hanyuu of Higurashi no Naku Koro ni is the true identity of Oyashiro-sama, and she takes the form of a young girl, appearing no older than Satoko or Rika.
Ivy (The Archive) in the Dresden Files contains the entire wealth of any knowledge that has ever been written down in any language throughout time... in the body of an 8-year old girl... who likes kitties.
It is implied in Demon The Fallen fluff that the (old) WorldOfDarknessGod is a girl. Since the Fallen are pretty much the only still-living beings who have actually seen God at the dawn of time, their word can be trusted.
Since the vast majority of the Fallen are still really, really pissed at God, don't put too much stock in their word.
God also has an evil sister named Oblivion, short for "The Grand Maw of Oblivion." Grand Maw wanted to create her own universe, and saying that she "failed" is not putting it strongly enough. Now she and her "offspring" spend their time gnawing underneath the afterlife until the end of the world.
And hey, Kanako Yasaka, why not, even though she's not as young-looking. Reality Warper Yukari Yakumo also may qualify. She's not God. But she might as well be.
Taken to the extreme in Ar tonelico series. Humans (and more) live in three gigantic towers that are also massive computers capable of potent magic [sic]. The Administrators of the towers are all little girls, especially Frelia.
Interestingly, the Satan(?) equivalent of Ar tonelico 1 Myuru/Jakuri is also a little girl.
Oracle of Tao has Ambrosia, who for much of the first game is oblivious that she is God's avatar (she's about 20-30 though). This creates an odd situation, since she was literally sending herselfon a quest. Later on though, she accepts being God fully, and the current version of God gets reincarnated so that Ambrosia can have a life with Nevras while her mother can have a life with God.
A sort-of inversion: In Strange Journey, Lucifer appears as a little blonde girl in white dress, calling herself "Louisa Ferre."
minus. isn't really confirmed to be God in the comic - just a girl with limitless unexplained powers.
But she does create the Afterlife, and is shown to run it whenever she isn't busy having fun.
An old, discontinued webcomic, Acid Reflux, had a little deity girl get her own (used) universe as a present. Her name, of course, was "God". Much humor occurs when she's sucked into said universe, a sort of high fantasy pastiche.
