Well... two stories came to mind, but...
When a young man contracts Fem Flu, the mysterious phenomenon that turns men into women, he immediately realizes this is the best thing to ever happen to him. However, that presents this now-woman with a different problem: there's only one known way to make these changes permanent, and that's to...
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This one's ongoing, and the MC has not yet become pregnant, but the premise kind of hinges around that, so it
probably will happen at some point?
When Pwalu's wife Qesem came home from the village, nine months pregnant after only being gone for a few hours, he thought she'd simply fallen afoul of a time warp. Unfortunate, but understandable. The village midwife said she and the baby seemed healthy. But when the months dragged on and...
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This one is weird, and I guess technically the MC doesn't become pregnant? but, she sort of does... you'd have to read it I think.
That said, after browsing my read stories list, I found one that
actually features a pregnancy!
Imprisoned, transformed, and mind-controlled by a monster, he had barely managed to escape, and managed to find a safe haven. But could the good witches give him back what he had lost? And did he even want it?
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... It isn't quite typical, but it's there! And a pivotal part of the plot, too, if not
quite as central to it as the other two.
... You'd think, given how many transfem stories I read and how common a fantasy that is, that there'd be more, but that's all I'm finding.
Edit: I thought of another, if you're cool with weird alien pregnancy:
Daniel is an asteroid miner who hooks up with an 8' tall alien hitchhiker and, after the condom breaks, learns that her species can sometimes mate with others. Unfortunately, she can't be the one to carry the eggs, so it looks like he'll have to do it... Chapters: 21 · Word Count: 96,934 ·...
fluff4.me
That one has the advantage of it actually being the MC's own kids.