Percentile means the percentage of people that you exceed amongst the population. This applies to anything, not just chess.
For example: Let's say in your highschool, there are 500 people in your class (let's assume you are a senior, class of 2015).
Amongst the 500 students, you are ranked 36th in the class. You are "better than" 464 students. You divide 464 by 500 and always round down! Therefore, there is no such thing as the 100th percentile. 99th is the highest. So here, 464/500 is .928, or 92.8%, which again, always rounding down, you are considered to be in the 92nd percentile in your class.
The top student would be in the 99th percentile as you can't be better than yourself, so you are better than 499 out of 500, or 499/500 = .998 = 99.8% = 99th Percentile
So for chess players, let's say you have 1,000,000 active players on chess.com. Let's say the highest rated player is rated 2900, and the second highest player is rated 2347, and everyone is below that. It doesn't matter that the second ranked person is a full 553 rating points below the top dog, he is still in the 99th percentile (999,998/1,000,000 = .999998, or 99.9998%, rounded down, is 99th Percentile)
Hope this clears up what is meant by "Percentile".
Hello. The one in the stats page. I thought it't percentage from the highest rating but it's not.