I can think of a couple of things you can try, but you don't give a lot of details to go on. While in Safari, pull down the "View" menu and select to show or hide the Toolbar, Bookmarks, Tab, and Status Bars.
If you don't have a View menu at the top, then you are missing the Apple menu. This might be because you are in Full Screen Mode (also under the "View" menu). To get out of it, press the esc key.
Neither of these types of hidden menus pop up when I move my cursor, though, but I don't know what operating system you are using and it might be different from mine.
If it still doesn't work, some more info (your OS and exactly what menus are disappearing) would be helpful.