POPFile will check at regular intervals of one hour whether entries have to be purged from the history. If this doesn't happen with your installation, the most likely reason is that POPFile isn't running continously. If you run POPFile, get your email, disconnect, and then close POPFile immediately, your history will keep on growing.
Possible solutions:
Give POPFile some time. Let it run for at least one hour and it should then delete any history entries that are old enough.
If you do not want to wait for an hour, you can use the “Delete now” checkbox on the Configuration page to make POPFile (0.22.0 or later) check if it is time to purge old entries. Just tick that box and click the “Apply” button to make POPFile remove messages older than the specified limit (the default limit is 2 days)
Purge the history manually by clicking on “Remove All” or “Remove Page” in the POPFile UI.