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Although in Windows F5 is the common (though not at all mnemonically appropriate!) keystroke to refresh the contents of a window, I've seen at least two different applications that use F9. One is the much-maligned Lotus Notes (which is actually quite good if you can overlook the abysmal user interface ;), and the other is muCommander.

Since Lotus Notes has other non-standard conventions that apparently are borrowed from other places (such as Esc to close a Window) and because it's unlikely to be a source of influence for many applications, I'm betting both apps borrow from a common source (even if indirectly). What is that source? Where does F9 as the refresh key come from?

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In addition to the answer from Synetech, I want to add that Microsoft QBASIC used F5 as the key for re-running the application from the point where it was stopped. This was essentially a 'refesh' of the written script to run. Using Shift+F5 would run the script from the beginning.

QBASIC used the old MS-DOS Edit application for word processing. F1 was already used for Help, and F3 was used for Find. I have no evidence of this, but F5 was likely used because it was the first key after the F1 through F4 series and was easy to locate because of the space between each four function keys.

Programmers familiar with this and other compilers that used F5 for running or 'refreshing' their scripts and recompiling their programers were likely responsible for this transition to F5 being for a page refresh.

Now, when you have the first F5 taken, the only remaining option is F9 as the first item in the block. This is more of an explanation of F5 history, but it may have been due to F5 being used for something different such as file saves.

A Google search reveals history about F5 and F9 in Notes and Excel.

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A quick check (F9 refresh) seems to indicate that it comes primarily from Microsoft Excel where it is used to refresh the calculations in the spreadsheet. Excel is an important part of the Microsoft Office suite, and seems to have been adopted throughout the suite for refreshing (e.g., Word and Outlook) at some point in the past until eventually being replaced by Windows’ own F5 for a more consistent user experience.

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My bet is from old-school accounting and finance software where it often meant recalculate (not technically refresh)...

MS Excel still uses this today for recalculate.

Also there is this accounting software company named after F9 :

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