Delete Frequently Visited on macOS Safari

1. Quit Safari, then open the app again while holding the Shift key on your keyboard.
   
2. Restart your Mac by clicking the Apple  menu in the upper left of the screen and choosing "Restart..."
   
3. Try clearing your browser history while in safe mode. Information on safe mode, and how to boot to it, can be found here: Use safe mode to isolate issues with your Mac
   
4. Test clearing the frequently visited site list in a new user account. An explanation of why this step can be helpful, and how to create a new user, is detailed in this article: How to test an issue in another user account on your Mac

Take cursor on top menu bar > Select History and hold option key .

Another window appears it depends on you how do you define frequently visited websites history to be cleared the last hour , today , today and yesterday , select any one according to the requirement and click on clear history .

well if the problem is you don't want to see the Frequently visited...then deactivate it. Open safari, on the top bar click on bookmarks you'll see the option show frequently visited in favorites . Unchecked and done. Thats if you use the favorites section but I guess it works for everything else.