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Jewell said: "It is beyond belief really that he hasn't had a look in for either the Under-20s or Under-21s.
"Leighton has been outstanding for us and was there or there abouts in our first team for most of last season.
"He has started well this time too, yet has still been overlooked."
The teenager had another good game in Sunday's win at West Ham, marking Sergei Rebrov in the first half and Luke Chadwick after the break.
Baines kept both wingers quiet, further pressing his claim for an international call-up.
The latest Under-21 squad for tonight's friendly with Ukraine at Middlesbrough's Riverside Stadium included a number of players from Championship clubs, but not Baines
Jewell said: "If Leighton played for anyone else and not Wigan, I'm sure he would be in the England Under-20s or Under-21s. It is an absolute disgrace that they don't even know who he is.
"In my opinion he is one of the best young left-backs we have got in this country at First Division (Championship) level.
"When I challenged one of the FA men last season about him, his response was 'Leighton who?' Never mind 'Leighton who', I think it is a case of 'Wigan who'.
"In some ways it doesn't surprise me because I see some of the guys who are FA coaches.
"They come to matches to chat to some old friends and don't even watch the game.
"I'm probably talking my way into trouble saying this, but it is how I feel about the situation.
"I don't really know what Leighton has to do.He is doing well enough at the minute and is working hard to stay in our team at Wigan.
"No doubt he'll get a call-up when he gets left out here!"
Meanwhile, Jewell is set to include recent signing Emerson Thome in tomorrow afternoon's Pontins League Premier Division clash against Preston at the Robin Park Arena.
The Brazilian defender was an unused substitute at West Ham and a run out in the reserves is designed to bolster his match fitness.
Jewell said: "Emerson is still a little bit behind the others with his fitness and needs some football now.
"It's okay being a big signing but he has to be fit, otherwise he wouldn't be able to do himself justice or more importantly, the team justice.
"He is getting closer every day to pushing the two lads who have the shirts at the minute for their places.
"I put him on the bench on Sunday because centre-half is a position in which we didn't have any cover, and if one of the lads had taken a knock, it could have left us short.
"We worked him hard in training last week, we'll work him hard again this week, and hopefully a game in the reserves will do him good."
Thome joined Latics on the eve of the season after failing to agree a new contract at neighbours Bolton.
The fact he wasn't with a club during the summer and unable to do pre-season training has left him still catching up in the fitness stakes.