Maybe bring a female friend with you? Or just say you're buying a gift. You could also bring something from the men's department with you in the dressing room so it'll look like you're trying it on.
Maybe get a female friend to go with you so they think that you are helping her get jeans.
Hmm, I don't see why you should feel uncomfortable as you shouldn't worry about other people's judgements :). Just think of it this way, you may be purchasing something for a friend. Also if you want to try them on, take a couple of mens items in with you and no one will be able to tell :) Good luck, hope it all works out
Have a female friend go shopping with you so it's not uncomfortable for you to go on the female section. Take the pants you like and a couple shirts or something and go to the dressing room so it's not completely obvious you've got the pants with ya! If I were you, I'd just try my best to step out of my comfort zone if it meant looking good later on! I understand it can be difficult. Good luck!
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Start eating more and put on some weight. Maybe then you'll be allowed to shop in the men's department.