Honestly, I'm always a bit surprised when someone goes looking specifically for that premise. It's one of those 'what ifs' that can go in a hundred directions—are they hiding it from Ron and the Weasleys? From the Ministry? Is it a marriage of convenience for political protection? Or a genuine secret love story? The flavor of the story completely changes based on that.
For the widest net, I'd hit Archive of Our Own first. The tagging system is your friend. Search for the relationship tag 'Harry Potter/Hermione Granger,' then filter by tags like 'Secret Relationship,' 'Marriage of Convenience,' or 'Secret Marriage.' Sometimes authors tag it as 'Undercover Marriage' or 'Fake Marriage,' which can overlap. You might also add 'Angst' or 'Drama' if you want that tension of keeping the secret.
FanFiction.net is more of a treasure hunt since the filtering is clunkier. You'd go into the Harry Potter category, sort by favorites or reviews for that ship to find the more established stories, and then comb through summaries. Look for phrases like 'hidden vows' or 'a union no one knows about.' A lot of the classic Harmony fics from the mid-2000s are there, and some might have this plot.
Don't overlook specific recommendation threads on places like r/HPfanfiction on Reddit or the Harry Potter forums on SpaceBattles or Sufficient Velocity. People often ask for 'secret marriage' fics, and you'll get curated lists with links. I found a decent one called 'Unlike a Sister' that way, though the secrecy element there is more emotional than formal.
My personal hang-up with this trope is when the secret feels contrived just for drama. I prefer it when the reason for secrecy is woven into a larger plot, like during a war or against a discriminatory law. It makes the stakes feel real, not just soap-opera stuff.