It affects your stat boost when you level up depending on when you train it. If you wait to Level 90 to EV train a Pokemon and finish it before go up to 91, you'll notice a huge increase in the stat that you are EV training in.
On the other hand, if you are EV training at a lower level like Level 20, the stat boost won't be as noticeable but you will eventually gain the rest of the stat boost as your Pokemon levels up.