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.