In my case I needed to do this interactively. The previous answers gave me the right functions to call, then it was just a matter of wrapping it a little to make them interactive:
(defun func-region (start end func)
"run a function over the region between START and END in current buffer."
(save-excursion
(let ((text (delete-and-extract-region start end)))
(insert (funcall func text)))))
(defun hex-region (start end)
"urlencode the region between START and END in current buffer."
(interactive "r")
(func-region start end #'url-hexify-string))
(defun unhex-region (start end)
"de-urlencode the region between START and END in current buffer."
(interactive "r")
(func-region start end #'url-unhex-string))
Add salt, I mean bind to keys according to taste.