Yes we use that phrase all the time. "Have you already been to Japan?", "Have you already been to the United States?" another way we would likely phrase the same idea is "Have you gone to ... yet/before?". For example "Have you gone to Japan before?", "Have you gone to Australia yet?". I hope this helps.
I feel the need to contribute here to help ensure that you are being given accurate and reliable information.
If you simply want to ask ...行ったことはある？
the most common way to do this is "have you ever been to ...?"
"have you been to ...?" is also common.
The phrase "have you already been to ...?" would be most commonly used in a situation where the person you are asking had previously expressed an intention to go to that place. For example, you could ask "Have you already been to the store?" of a person who had previously said that they were planning to go there.