1
general::
Also, pain in the ass or butt. A source of annoyance, a nuisance, as in Joan is a real pain in the neck, with her constant complaining, or Jack told his brother to stop being a pain in the ass. The first of these colloquial expressions dates from about 1900 and originated as a euphemism for the two less polite variants.
American Heritage Idioms
2
general::
Phrase(s): a pain in the neck
Fig. a bother; an annoyance. • This assignment is a pain in the neck. • Your little brother is a pain in the neck.
McGrawhill's American Idioms And Phrasal Verbs