I'm all for medicating on a flight. The advil will help her with any ear pain too. Try not worry, I know it's easier said than done. We've flown with DS when he was 5 months (he slept the whole time), when he was 18 mths old, he slept all the way there and watched his DVD's on the way home and just last month when he was 2.5. He didn't sleep much, but watched "Cars" and looked at books. But just in case, 30 min before each flight he got Tylenol with a decongestant. He's had ear infections a lot lately, but didn't complain of any ear pain. He was coming down with a cold on the way there, so the Tylenol helped with that too.
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I second this. I always keep Benedryl fast melts in the bag as a backup. It will probably be fine and you won't need them, but just in case you have them. Just make sure whatever you bring they have had before, so you know what reactions they might have. The worst would be to give them something and have them become super hyper!