This doesn't have a the boy writing one the desk but the plot is similar to what you described:
http://www.mangago.me/read-manga/samishigariya_no_love_letter/
http://www.mangago.me/read-manga/miracle_time/
Main person is a girl, but is very close to what you're explaining.
I don't think it's this but it has the writing on the desk thing you mentioned
http://www.mangago.me/read-manga/junjou_romantica/
Yeah it's something like that. But it's a boy. I can't remember if they meet each other
Im looking for a oneshot. Where this highschool boy writes on his desk and someone write back and it someone from the past and the boy was suppose to meet the mystery person in present. Can anyone help?