Safari history keeps reappearing even after deleting.

If this persists, is removing all internet history an option? Safari > History > Clear History and Website Data. (This will remove literally ALL website data, be warned)

However try the following: Head to History > Show History in the Safari menu bar. Alternatively, you can use the default shortcut Option-Command-2 to take you to the same place.

Here, you’ll see a list of all of your browser history organized by date, with the most recently visited websites at the top. Ignore that “Clear History” button at the bottom of the window, because that works just like the “Clear History and Website Data” function mentioned earlier. Instead, press Command-A to select all of the entries, and just hit Delete on your keyboard. This manually selects and deletes all of your browser history, but leaves website data intact, just like the old “Clear History” function in earlier versions of Safari.

If you’d prefer to selectively clear just some of your browser history, the Show History window allows for that, too. So, instead of using Command-A to select all, just hold the Command key and click on each history entry you wish to delete (or hold Shift while clicking the first and last in a series of contiguous items). When they’re all selected, you can then press Delete on my keyboard to delete only the desired history items.

http://www.tekrevue.com/tip/clear-history-but-not-website-data-safari/

Hope this helps.

Back up all data before proceeding.

This procedure will unlock all your user files (not system files) and reset their ownership, permissions, and access controls to the default. If you've intentionally set special values for those attributes on any of your files, they will be reverted. In that case, either stop here, or be prepared to recreate the settings if necessary. Do so only after verifying that those settings didn't cause the problem. If none of this is meaningful to you, you don't need to worry about it, but you do need to follow the instructions below.

Step 1

If you have more than one user, and the one in question is not an administrator, then go to Step 2.

Triple-click anywhere in the following line on this page to select it:

sudo find ~ $TMPDIR.. -exec chflags -h nouchg,nouappnd,noschg,nosappnd {} + -exec chown -h $UID {} + -exec chmod +rw {} + -exec chmod -h -N {} + -type d -exec chmod -h +x {} + 2>&-

Copy the selected text to the Clipboard by pressing the key combination command-C.

Launch the built-in Terminal application in any of the following ways:

☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)

☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.

☞ Open LaunchPad and start typing the name.

Paste into the Terminal window by pressing command-V. I've tested these instructions only with the Safari web browser. If you use another browser, you may have to press the return key after pasting.

You'll be prompted for your login password, which won't be displayed when you type it. Type carefully and then press return. You may get a one-time warning to be careful. If you don’t have a login password, you’ll need to set one before you can run the command. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.

The command may take several minutes to run, depending on how many files you have. Wait for a new line ending in a dollar sign ($) to appear, then quit Terminal.

Step 2 (optional)

Take this step only if you have trouble with Step 1, if you prefer not to take it, or if it doesn't solve the problem.

Start up in Recovery mode. When the OS X Utilities screen appears, select

Utilities ▹ Terminal

from the menu bar. A Terminal window will open. In that window, type this:

resetp

Press the tab key. The partial command you typed will automatically be completed to this:

resetpassword

Press return. A Reset Password window will open. You’re not going to reset a password.

Select your startup volume ("Macintosh HD," unless you gave it a different name) if not already selected.

Select your username from the menu labeled Select the user account if not already selected.

Under Reset Home Directory Permissions and ACLs, click the Reset button.

Select

 ▹ Restart

from the menu bar.

Well as you are only trying to remove a few I would recommend going for the full Website Data Removal; Safari > History > Clear History and Website Data.

I would also recommend that along with the above, you also go into your Cookie Settings; Safari > Preferences > Privacy. Edit your settings as you please, however for the sake of permanently deleting your history, change to not accepting Cookies, then try the full website data removal again.

Top this off with a Safari/System Re-Boot; Right Click Safari App > Quit Safari.

Hope this helps.

Do you synchronize Safari with another device via iCloud?