Check your PC for any and all forms of programs that you can use to remote control your PC with your smartphone (eg, Monect, PC Remote), and disable all services and devices associated with them - for some reason these programs interfere with the controller inputs to the game.

Command line disable for Monect programs:
> Open admin command prompt. (press WindowsKey+X, then A, or right-click command prompt and select Run as Administrator)
> Type the following commands exactly as written, press enter after each one:

sc config "monectdevices" start=disabled

sc stop "monectdevices"

The second command may report as failed if the service was not running, this is fine.

Go to Start > search Device Manager and open it, navigate to Human Interface Devices, double click each item in the list and look for any that refer to "Monect" in the general tab of the popup window (see example below) and disable them.



Restart your PC after following these steps, then try your controller in Sekiro again.

NOTE: This probably won't fix your problem if you haven't used these kinds of programs on your PC before, it's just what ended up being the culprit in my case. I hope this gets patched eventually, it's odd that Sekiro seems to be the only game I've ever encountered that's affected by it.